Microstructure of chemically modified wood using X-ray computed tomography in relation to wetting properties

X-ray computed tomography (XCT) was utilized to visualize and quantify the 2D and 3D microstructure of acetylated southern yellow pine (pine) and maple, as well as furfurylated pine samples. The total porosity and the porosity of different cell types, as well as cell wall thickness and maximum opening of tracheid lumens were evaluated. The wetting properties (swelling and capillary uptake) were related to these microstructural characteristics. The data show significant changes in the wood structure for furfurylated pine sapwood samples, including a change in tracheid shape and filling of tracheids by furan polymer. In contrast, no such changes were noted for the acetylated pine samples at the high resolution of 0.8 mu m. The XCT images obtained for the furfurylated maple samples demonstrated that all ray cells and some vessel elements were filled with furan polymer while the fibers largely remained unchanged. Furfurylation significantly decreased the total porosity of both the maple and pine samples. Furthermore, this was observed in both earlywood (EW) and latewood (LW) regions in the pine samples. In contrast, the total porosity of pine samples was hardly affected by acetylation. These findings are in line with wetting results demonstrating that furfurylation reduces both swelling and capillary uptake in contrast to acetylation which reduces mostly swelling. Furfurylation significantly increased the cell wall thickness of both the maple and pine samples, especially at higher levels of furfurylation

Detection of genetically modified plant products by protein strip testing: an evaluation of real-life samples

The determination of the presence of genetically modified plant material by the detection of expressed genetically engineered proteins using lateral flow protein strip tests has been evaluated in different matrices. The presence of five major genetically engineered proteins (CP4-EPSPS, CryIAb, Cry9C, PAT/pat and PAT/bar protein) was detected at low levels in seeds, seed/leaf powder and leaf tissue from genetically modified soy, maize or oilseed rape. A comparison between &quot;protein strip test&quot; (PST) and &quot;polymerase chain reaction&quot; (PCR) analysis of genetically modified food/feed samples demonstrates complementarities of both techniques. -® Springer-Verlag 2007</p

Validating module network learning algorithms using simulated data

In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a software package for learning module networks, called LeMoNe, which incorporates a novel strategy for learning regulatory programs. Novelties include the use of a bottom-up Bayesian hierarchical clustering to construct the regulatory programs, and the use of a conditional entropy measure to assign regulators to the regulation program nodes. Using SynTReN data, we test the performance of LeMoNe in a completely controlled situation and assess the effect of the methodological changes we made with respect to an existing software package, namely Genomica. Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance. Overall, application of Genomica and LeMoNe to simulated data sets gave comparable results. However, LeMoNe offers some advantages, one of them being that the learning process is considerably faster for larger data sets. Additionally, we show that the location of the regulators in the LeMoNe regulation programs and their conditional entropy may be used to prioritize regulators for functional validation, and that the combination of the bottom-up clustering strategy with the conditional entropy-based assignment of regulators improves the handling of missing or hidden regulators.Comment: 13 pages, 6 figures + 2 pages, 2 figures supplementary informatio

Biomass increment and carbon sequestration in hedgerow-grown trees

The global role of tree-based climate change mitigation is widely recognized; trees sequester large amounts of atmospheric carbon, and woody biomass has an important role in the future biobased economy. In national carbon and biomass budgets, trees growing in hedgerows and tree rows are often allocated the same biomass increment data as forest-grown trees. However, the growing conditions in these linear habitats are different from forests given that the trees receive more solar radiation, potentially benefit from fertilization residuals from adjacent fields and have more physical growing space. Tree biomass increment and carbon storage in linear woody elements should therefore be quantified and correctly accounted for. We examined four different hedgerow systems with combinations of pedunculate oak, black alder and silver birch in northern Belgium. We used X-ray CT scans of pith-to-bark cores of 73 trees to model long-term (tree life span) and short-term (last five years) trends in basal area increment and increment in aboveground stem biomass. The studied hedgerows and tree rows showed high densities (168–985 trees km-1) and basal areas (22.1–44.9 m2 km-1). In all four hedgerow systems, we found a strong and persistent increase in stem biomass and thus carbon accumulation with diameter (long-term trend). The current growth performance (short-term trend) also increased with tree diameter and was not related to hedgerow tree density or basal area, which indicates that competition for light does not (yet) limit tree growth in these ecosystems. The total stem volume was 82.0–339.7 m3 km-1 (corresponding to 18.8–100.7 Mg aboveground carbon km-1) and the stem volume increment was 3.1–14.5 m3 km-1 year-1 (aboveground carbon sequestration 0.7–4.3 Mg km-1 year-1). The high tree densities and the persistent increase in growth of trees growing in hedgerow systems resulted in substantial wood production and carbon sequestration rates at the landscape scale. Our findings show that trees growing in hedgerow systems should be included when biomass and carbon budgets are drafted. The biomass production rates of hedgerow trees we provide can help refine the IPCC Guidelines for National Greenhouse Gas Inventories

Use of pJANUS™-02-001 as a calibrator plasmid for Roundup Ready soybean event GTS-40-3-2 detection: an interlaboratory trial assessment

Owing to the labelling requirements of food and feed products containing materials derived from genetically modified organisms, quantitative detection methods have to be developed for this purpose, including the necessary certified reference materials and calibrator standards. To date, for most genetically modified organisms authorized in the European Union, certified reference materials derived from seed powders are being developed. Here, an assessment has been made on the feasibility of using plasmid DNA as an alternative calibrator for the quantitative detection of genetically modified organisms. For this, a dual-target plasmid, designated as pJANUS™-02-001, comprising part of a junction region of genetically modified soybean event GTS-40-3-2 and the endogenous soybean-specific lectin gene was constructed. The dynamic range, efficiency and limit of detection for the soybean event GTS-40-3-2 real-time quantitative polymerase chain reaction (Q-PCR) system described by Terry et al. (J AOAC Int 85(4):938–944, 2002) were shown to be similar for in house produced homozygous genomic DNA from leaf tissue of soybean event GTS-40-3-2 and for plasmid pJANUS™-02-001 DNA backgrounds. The performance of this real-time Q-PCR system using both types of DNA templates as calibrator standards in quantitative DNA analysis was further assessed in an interlaboratory trial. Statistical analysis and fuzzy-logic-based interpretation were performed on critical method parameters (as defined by the European Network of GMO Laboratories and the Community Reference Laboratory for GM Food and Feed guidelines) and demonstrated that the plasmid pJANUS™-02-001 DNA represents a valuable alternative to genomic DNA as a calibrator for the quantification of soybean event GTS-40-3-2 in food and feed products