Jan Van den Bulcke
Ghent University
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Featured researches published by Jan Van den Bulcke.
Microscopy and Microanalysis | 2009
Jan Van den Bulcke; Matthieu Boone; Joris Van Acker; Luc Van Hoorebeke
As wood is prone to fungal degradation, fundamental research is necessary to increase our knowledge aiming at product improvement. Several imaging modalities are capable of visualizing fungi, but the X-ray equipment presented in this article can envisage fungal mycelium in wood nondestructively in three dimensions with submicron resolution. Four types of wood subjected to the action of the white rot fungus Coriolus versicolor (Linnaeus) Quélet (CTB 863 A) were scanned using an X-ray-based approach. Comparison of wood volumes before and after fungal exposure, segmented manually or semiautomatically, showed the presence of the fungal mass on and in the wood samples and therefore demonstrated the usefulness of computed X-ray tomography for mycological and wood research. Further improvements to the experimental setup are necessary to resolve individual hyphae and enhance segmentation.
Annals of Forest Science | 2009
Jan Van den Bulcke; Matthieu Boone; Joris Van Acker; Marc Stevens; Luc Van Hoorebeke
Abstract• Wood identification, anatomical examination and retrieval of quantitative information are important aspects of many research disciplines. Conventional light microscopy with a camera and (semi)-automatic image analysis software is an often used methodology for these purposes. More advanced techniques such as fluorescence, scanning electron, transmission electron, confocal laser scanning and atomic force microscopy are also part of the toolset answering to the need for detailed imaging.• Fast, non-destructive visualization in three dimensions with high resolution combined with a broad field of view is sought-after, especially in combination with flexible software.• A highly advanced supplement to the existing techniques, namely X-ray sub-micron tomography, meets these requirements. It enables the researcher to visualize the material with a voxel size approaching < 1 μm for small samples (< 1 mm). Furthermore, with tailor-made processing software quantitative data about the wood in two and three dimensions can be obtained. Examples of visualization and analysis of four wood species are given in this paper, focusing on the opportunities of tomography at micron and sub-micron resolution.• X-ray computed tomography offers many possibilities for material research in general and wood science in specific, as a qualitative as well as a quantitative technique.Résumé• L’identification du bois, l’observation anatomique et l’obtention d’informations quantitatives sont des aspects importants dans différentes disciplines scientifiques. La microscopie optique conventionnelle couplée à l’acquisition et au traitement semi automatique des images est souvent utilisée pour atteindre ces objectifs. Des techniques plus récentes comme la fluorescence, la microscopie électronique par balayage ou par transmission, la microscopie confocale ou encore à force atomique constituent une panoplie d’outils répondant à ces besoins d’imagerie fine.• Il y a une forte demande d’outils non destructifs de visualisation 3D à haute résolution combinés à un large champ de vision et surtout avec des logiciels flexibles.• En complément avancé à ces techniques la tomographie RX submicrométrique remplit ces conditions. Elle permet au chercheur de visualiser le matériau avec une taille de voxel inférieure au micron pour de petits échantillons dont la taille est inférieure au mm. En outre, à l’aide de logiciels de traitement adaptés, des données quantitatives peuvent être obtenues pour le bois en deux et trois dimensions. Dans ce papier on présente des exemples de visualisation et d’analyse pour quatre essences en focalisant sur les possibilités de tomographie aux échelles micrométrique et submicrométrique.• La tomographie RX offre de nombreuses possibilités pour la recherche en science des matériaux en général et en sciences du bois en particulier, que ce soit pour les approches qualitatives ou pour les approches quantitatives.
Annals of Botany | 2012
Agathe Die; Peter Kitin; François N’Guessan Kouamé; Jan Van den Bulcke; Joris Van Acker; Hans Beeckman
BACKGROUND AND AIMS Teak forms xylem rings that potentially carry records of carbon sequestration and climate in the tropics. These records are only useful when the structural variations of tree rings and their periodicity of formation are known. METHODS The seasonality of ring formation in mature teak trees was examined via correlative analysis of cambial activity, xylem and phloem formation, and climate throughout 1·5 years. Xylem and phloem differentiation were visualized by light microscopy and scanning electron microscopy. KEY RESULTS A 3 month dry season resulted in semi-deciduousness, cambial dormancy and formation of annual xylem growth rings (AXGRs). Intra-annual xylem and phloem growth was characterized by variable intensity. Morphometric features of cambium such as cambium thickness and differentiating xylem layers were positively correlated. Cambium thickness was strongly correlated with monthly rainfall (R(2) = 0·7535). In all sampled trees, xylem growth zones (XGZs) were formed within the AXGRs during the seasonal development of new foliage. When trees achieved full leaf, the xylem in the new XGZs appeared completely differentiated and functional for water transport. Two phloem growth rings were formed in one growing season. CONCLUSIONS The seasonal formation pattern and microstructure of teak xylem suggest that AXGRs and XGZs can be used as proxies for analyses of the tree history and climate at annual and intra-annual resolution.
Annals of Botany | 2011
Maaike De Ridder; Jan Van den Bulcke; Dries Vansteenkiste; Denis Van Loo; Manuel Dierick; Bert Masschaele; Yoni De Witte; David Mannes; Eberhard Lehmann; Hans Beeckman; Luc Van Hoorebeke; Joris Van Acker
BACKGROUND AND AIMS Density is a crucial variable in forest and wood science and is evaluated by a multitude of methods. Direct gravimetric methods are mostly destructive and time-consuming. Therefore, faster and semi- to non-destructive indirect methods have been developed. METHODS Profiles of wood density variations with a resolution of approx. 50 µm were derived from one-dimensional resistance drillings, two-dimensional neutron scans, and three-dimensional neutron and X-ray scans. All methods were applied on Terminalia superba Engl. & Diels, an African pioneer species which sometimes exhibits a brown heart (limba noir). KEY RESULTS The use of X-ray tomography combined with a reference material permitted direct estimates of wood density. These X-ray-derived densities overestimated gravimetrically determined densities non-significantly and showed high correlation (linear regression, R(2) = 0·995). When comparing X-ray densities with the attenuation coefficients of neutron scans and the amplitude of drilling resistance, a significant linear relation was found with the neutron attenuation coefficient (R(2) = 0·986) yet a weak relation with drilling resistance (R(2) = 0·243). When density patterns are compared, all three methods are capable of revealing the same trends. Differences are mainly due to the orientation of tree rings and the different characteristics of the indirect methods. CONCLUSIONS High-resolution X-ray computed tomography is a promising technique for research on wood cores and will be explored further on other temperate and tropical species. Further study on limba noir is necessary to reveal the causes of density variations and to determine how resistance drillings can be further refined.
Holzforschung | 2010
Liesbeth De Vetter; Jan Van den Bulcke; Joris Van Acker
The interaction of wood with water is a primary factor for degradation of the substrate. Organosilicons are known to behave like a water repellent, thus they are in discussion as protecting agents for wood used outdoors. In the present paper, the influence of water on organosilicon treated material was investigated. Solid Scots pine sapwood was impregnated or treated superficially with low concentrations of organosilicons and evaluated for several water related characteristics. The results confirm the water repellent properties of organosilicons as the polysiloxane film increases the contact angle between water and the wood substrate. However, they do not influence the total uptake of moisture but can change the rate at which moisture is taken up, and as such, prolong the service life of the substrate. In general, impregnated specimens behave better than dipped ones. To gain more insight in the exact behavior, continuous moisture uptake experiments are needed in real outdoor exposure tests.
Molecular & Cellular Proteomics | 2016
Wim Jonckheere; Wannes Dermauw; Vladimir Zhurov; Nicky Wybouw; Jan Van den Bulcke; Carlos A. Villarroel; Robert Greenhalgh; Mike Grbić; Robert C. Schuurink; Luc Tirry; Geert Baggerman; Richard M. Clark; Merijn R. Kant; Bartel Vanholme; Gerben Menschaert; Thomas Van Leeuwen
The two-spotted spider mite Tetranychus urticae is an extremely polyphagous crop pest. Alongside an unparalleled detoxification potential for plant secondary metabolites, it has recently been shown that spider mites can attenuate or even suppress plant defenses. Salivary constituents, notably effectors, have been proposed to play an important role in manipulating plant defenses and might determine the outcome of plant-mite interactions. Here, the proteomic composition of saliva from T. urticae lines adapted to various host plants—bean, maize, soy, and tomato—was analyzed using a custom-developed feeding assay coupled with nano-LC tandem mass spectrometry. About 90 putative T. urticae salivary proteins were identified. Many are of unknown function, and in numerous cases belonging to multimembered gene families. RNAseq expression analysis revealed that many genes coding for these salivary proteins were highly expressed in the proterosoma, the mite body region that includes the salivary glands. A subset of genes encoding putative salivary proteins was selected for whole-mount in situ hybridization, and were found to be expressed in the anterior and dorsal podocephalic glands. Strikingly, host plant dependent expression was evident for putative salivary proteins, and was further studied in detail by micro-array based genome-wide expression profiling. This meta-analysis revealed for the first time the salivary protein repertoire of a phytophagous chelicerate. The availability of this salivary proteome will assist in unraveling the molecular interface between phytophagous mites and their host plants, and may ultimately facilitate the development of mite-resistant crops. Furthermore, the technique used in this study is a time- and resource-efficient method to examine the salivary protein composition of other small arthropods for which saliva or salivary glands cannot be isolated easily.
PLOS ONE | 2015
Jean-François Bastin; Adeline Fayolle; Yegor Tarelkin; Jan Van den Bulcke; Thalès de Haulleville; Frédéric Mortier; Hans Beeckman; Joris Van Acker; Adeline Serckx; Jan Bogaert; Charles De Cannière
Context Wood specific gravity is a key element in tropical forest ecology. It integrates many aspects of tree mechanical properties and functioning and is an important predictor of tree biomass. Wood specific gravity varies widely among and within species and also within individual trees. Notably, contrasted patterns of radial variation of wood specific gravity have been demonstrated and related to regeneration guilds (light demanding vs. shade-bearing). However, although being repeatedly invoked as a potential source of error when estimating the biomass of trees, both intraspecific and radial variations remain little studied. In this study we characterized detailed pith-to-bark wood specific gravity profiles among contrasted species prominently contributing to the biomass of the forest, i.e., the dominant species, and we quantified the consequences of such variations on the biomass. Methods Radial profiles of wood density at 8% moisture content were compiled for 14 dominant species in the Democratic Republic of Congo, adapting a unique 3D X-ray scanning technique at very high spatial resolution on core samples. Mean wood density estimates were validated by water displacement measurements. Wood density profiles were converted to wood specific gravity and linear mixed models were used to decompose the radial variance. Potential errors in biomass estimation were assessed by comparing the biomass estimated from the wood specific gravity measured from pith-to-bark profiles, from global repositories, and from partial information (outer wood or inner wood). Results Wood specific gravity profiles from pith-to-bark presented positive, neutral and negative trends. Positive trends mainly characterized light-demanding species, increasing up to 1.8 g.cm-3 per meter for Piptadeniastrum africanum, and negative trends characterized shade-bearing species, decreasing up to 1 g.cm-3 per meter for Strombosia pustulata. The linear mixed model showed the greater part of wood specific gravity variance was explained by species only (45%) followed by a redundant part between species and regeneration guilds (36%). Despite substantial variation in wood specific gravity profiles among species and regeneration guilds, we found that values from the outer wood were strongly correlated to values from the whole profile, without any significant bias. In addition, we found that wood specific gravity from the DRYAD global repository may strongly differ depending on the species (up to 40% for Dialium pachyphyllum). Main Conclusion Therefore, when estimating forest biomass in specific sites, we recommend the systematic collection of outer wood samples on dominant species. This should prevent the main errors in biomass estimations resulting from wood specific gravity and allow for the collection of new information to explore the intraspecific variation of mechanical properties of trees.
Biomedical Materials | 2016
Timothy Douglas; Agnieszka Dokupil; Katarzyna Reczyńska; Gilles Brackman; Małgorzata Krok-Borkowicz; Julia K. Keppler; Mojca Božič; Pascal Van Der Voort; Krzysztof Pietryga; Sangram Keshari Samal; Lieve Balcaen; Jan Van den Bulcke; Joris Van Acker; Frank Vanhaecke; Karin Schwarz; Tom Coenye; Elżbieta Pamuła
Hydrogels offer several advantages as biomaterials for bone regeneration, including ease of incorporation of soluble substances such as mineralization-promoting enzymes and antibacterial agents. Mineralization with calcium phosphate (CaP) increases bioactivity, while antibacterial activity reduces the risk of infection. Here, gellan gum (GG) hydrogels were enriched with alkaline phosphatase (ALP) and/or Seanol(®), a seaweed extract rich in phlorotannins (brown algae-derived polyphenols), to induce mineralization with CaP and increase antibacterial activity, respectively. The sample groups were unmineralized hydrogels, denoted as GG, GG/ALP, GG/Seanol and GG/Seanol/ALP, and hydrogels incubated in mineralization medium (0.1 M calcium glycerophosphate), denoted as GG/ALP_min, GG/Seanol_min and GG/Seanol/ALP_min. Seanol(®) enhanced mineralization with CaP and also increased compressive modulus. Seanol(®) and ALP interacted in a non-covalent manner. Release of Seanol(®) occurred in a burst phase and was impeded by ALP-mediated mineralization. Groups GG/Seanol and GG/ALP/Seanol exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus. GG/Seanol/ALP_min, but not GG/Seanol_min, retained some antibacterial activity. Eluates taken from groups GG/ALP_min, GG/Seanol_min and GG/ALP/Seanol_min displayed comparable cytotoxicity towards MG-63 osteoblast-like cells. These results suggest that enrichment of hydrogel biomaterials with phlorotannin-rich extracts is a promising strategy to increase mineralizability and antibacterial activity.
Journal of The Optical Society of America A-optics Image Science and Vision | 2013
Erik L. G. Wernersson; Matthieu Boone; Jan Van den Bulcke; Luc Van Hoorebeke; Cris L. Luengo Hendriks
With increased resolution in x-ray computed tomography, refraction adds increasingly to the attenuation signal. Though potentially beneficial, the artifacts caused by refraction often need to be removed from the image. In this paper, we propose a postprocessing method, based on deconvolution, that is able to remove these artifacts after conventional reconstruction. This method poses two advantages over existing projection-based (preprocessing) phase-retrieval or phase-removal algorithms. First, evaluation of the parameters can be done very quickly, improving the overall speed of the method. Second, postprocessing methods can be applied when projection data is not available, which occurs in several commercial systems with closed software or when projection data has been deleted. It is shown that the proposed method performs comparably to state-of-the-art methods in terms of image quality.
Annals of Botany | 2016
Tom De Mil; Astrid Vannoppen; Hans Beeckman; Joris Van Acker; Jan Van den Bulcke
BACKGROUND AND AIMS Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. METHODS Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. KEY RESULTS Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. CONCLUSIONS A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species.