Tree species traits cause divergence in soil acidification during four decades of postagricultural forest development

A change in land use from agriculture to forest generally increases soil acidity. However, it remains unclear to what extent plant traits can enhance or mitigate soil acidification caused by atmospheric deposition. Soil acidification is detrimental for the survival of many species. An in‐depth understanding of tree species‐specific effects on soil acidification is therefore crucial, particularly in view of the predicted global increases in acidifying nitrogen (N) deposition. Here, we report soil acidification rates in a chronosequence of broadleaved deciduous forests planted on former arable land in Belgium. This region receives one of the highest loads of potentially acidifying atmospheric deposition in Europe, which allowed us to study a ‘worst case scenario’. We show that less than four decades of forest development caused significant soil acidification. Atmospheric deposition undoubtedly and unequivocally drives postagricultural forests towards more acidic conditions, but the rate of soil acidification is also determined by the tree species‐specific leaf litter quality and litter decomposition rates. We propose that the intrinsic differences in leaf litter quality among tree species create fundamentally different nutrient cycles within the ecosystem, both directly through the chemical composition of the litter and indirectly through its effects on the size and composition of earthworm communities. Poor leaf litter quality contributes to the absence of a burrowing earthworm community, which retards leaf litter decomposition and, consequently, results in forest‐floor build‐up and soil acidification. Also nutrient uptake and N₂ fixation are causing soil acidification, but were found to be less important. Our results highlight the fact that tree species‐specific traits significantly influence the magnitude of human pollution‐induced soil acidification.     

Development of a novel ectonucleotidase assay suitable for high-throughput screening

5'-Ectonucleotidase (NT5E) catalyzes the conversion of adenosine monophosphate to adenosine and free phosphate. The role of this ectonucleotidase and its production of adenosine are linked with immune function, angiogenesis, and cancer. NT5E activity is typically assayed either by chromatographic quantification of substrates and products using high-performance liquid chromatography (HPLC) or by quantification of free phosphate using malachite green. These methods are not suitable for robust screening assays of NT5E activity. HPLC is not readily suitable for the rapid and efficient assay of multiple samples and malachite green is highly sensitive to the phosphate-containing buffers common in various media and sample buffers. Here the development and validation of a novel high-throughput ectonucleotidase screening assay are described, which makes use of a luciferase-based assay reagent, the Promega CellTiter-Glo kit, to measure the catabolism of AMP by NT5E. This multiwell plate-based assay facilitates the screening of potential ectonucleotidase antagonists and is unaffected by the presence of contaminating phosphate molecules present in screening samples.     

Self‐organised patchiness and scale‐dependent bio‐geomorphic feedbacks in aquatic river vegetation

Spatial self‐organisation of ecosystems is the process by which large‐scale ordered spatial patterns emerge from disordered initial conditions through local feedbacks between organisms and their environment. Such process is considered important for ecosystem functioning, providing increased productivity, resistance and resilience against environmental change. Although spatial self‐organisation has been found for an increasing number of ecosystems, it has never been shown so far for aquatic river vegetation. Here we explore the existence of spatial self‐organisation of freshwater macrophyte patches in a typical lowland river (Belgium), showing that the underlying mechanisms for pattern formation are scale‐dependent feedbacks between plant growth, water flow and local river bed erosion and sedimentation. The mapping of vegetation patches showed that the frequency distribution of patch sizes is governed by a power‐law function, suggesting that the patches are self‐organised. Scale‐dependent feedbacks, likely to lead to this self‐organised pattern, were demonstrated with a mimic experiment. Both positive and negative feedbacks on plants were confirmed by a transplantation experiment. Placing vegetation patch mimics in the river showed experimentally that on a short range (within and behind the mimics) flow reduction and increased sedimentation occurred, while on a larger range (next to patches) the flow was accelerated and decreased sedimentation took place. By transplanting macrophytes within, next to and further away from existing patches, it was proven that the conditions within the patches favoured the survival and growth of transplants (i.e. short‐range positive feedback), while the conditions just next to patches led to decreased survival and growth (i.e. long‐range negative feedback).     

Antagonistic cross-regulation between Wnt and Hedgehog signalling pathways controls post-embryonic retinal proliferation

Continuous neurogenesis in the adult nervous system requires a delicate balance between proliferation and differentiation. Although Wnt/β-catenin and Hedgehog signalling pathways are thought to share a mitogenic function in adult neural stem/progenitor cells, it remains unclear how they interact in this process. Adult amphibians produce retinal neurons from a pool of neural stem cells localised in the ciliary marginal zone (CMZ). Surprisingly, we found that perturbations of the Wnt and Hedgehog pathways result in opposite proliferative outcomes of neural stem/progenitor cells in the CMZ. Additionally, our study revealed that Wnt and Hedgehog morphogens are produced in mutually exclusive territories of the post-embryonic retina. Using genetic and pharmacological tools, we found that the Wnt and Hedgehog pathways exhibit reciprocal inhibition. Our data suggest that Sfrp-1 and Gli3 contribute to this negative cross-regulation. Altogether, our results reveal an unexpected antagonistic interplay of Wnt and Hedgehog signals that may tightly regulate the extent of neural stem/progenitor cell proliferation in the Xenopus retina.     

Distinguishing between turnover and nestedness in the quantification of biotic homogenization

Compositional changes through local extinction and colonization are inherent to natural communities, but human activities are increasingly influencing the rate and nature of the species being lost and gained. Biotic homogenization refers to the process by which the compositional similarity of communities increases over time through a non-random reshuffling of species. Despite the extensive conceptual development of the homogenization framework, approaches to quantify patterns of homogenization are scarcely developed. Most studies have used classical dissimilarity indices that actually quantify two components of compositional variation: turnover and nestedness. Here we demonstrate that a method that partitions those two components reveals patterns of homogenization that are otherwise obscured using traditional techniques. The forest understorey vegetation of an unmanaged reserve was recorded in permanent plots in 1979 and 2009. In only thirty years, the local species richness significantly decreased and the variation in the species composition from site to site shifted towards a structure with reduced true species turnover and increased dissimilarity due to nestedness. A classic analysis masked those patterns. In summary, we illustrated the need to move beyond the simple quantification of homogenization using classical indices and advocate integration of the multitude of ways to quantify community similarity into the homogenization framework.     

Intravenous and intradermal TriMix-dendritic cell therapy results in a broad T-cell response and durable tumor response in a chemorefractory stage IV-M1c melanoma patient

Dendritic cells (DCs) electroporated with mRNA encoding CD70, CD40L and a constitutively active toll-like receptor 4 (TriMix-DC) have an increased T-cell stimulatory capacity. In a prospective phase IB clinical trial, we treated melanoma patients with intradermal and intravenous injections of autologous TriMix-DC co-electroporated with mRNA encoding full-length MAGE-A3, MAGE-C2, tyrosinase and gp100. We report here the immunological and clinical results obtained in one patient with a particularly favorable outcome. This patient had stage IV-M1c melanoma with documented progression during dacarbazine chemotherapy and received 5 TriMix-DC injections. Following DC therapy, a broad CD8(+) T-cell response against multiple epitopes derived from all four treatment antigens was found in the blood and among T cells derived from DTH biopsy. In addition, CD4(+) T cells recognizing different MAGE-A3-derived epitopes were detected in DTH-derived cells. A spontaneous anti-MAGE-C2 CD8(+) T-cell response was present prior to TriMix-DC therapy and increased during treatment. The tumor response was assessed with 18-fluorodeoxyglucose-positron emission/computed tomography. We documented a partial tumor response according to RECIST criteria with a marked reduction in (18)F-FDG-uptake by lung, lymph node and bone metastases. The patient remains free from progression after 12 months of follow-up. This case report indicates that administration of autologous TriMix-DC by the combined intradermal and intravenous route can mediate a durable objective tumor response accompanied by a broad T-cell response in a chemorefractory stage IV-M1c melanoma patient.     

Immunization with N-propionyl polysialic acid–KLH conjugate in patients with small cell lung cancer is safe and induces IgM antibodies reactive with SCLC cells and bactericidal against group B meningococci

Purpose  

Polysialic acid (polySA) is a polymer side chain bound to the neural cell adhesion molecule that is extensively expressed on the surface of small cell lung cancer (SCLC) cells. In our previous study, a robust antibody response was noted in patients with SCLC after vaccination with 30 μg of keyhole limpet hemocyanin (KLH)-conjugated N-propionylated (NP-) polySA, but peripheral neuropathy and ataxia were detected in several vaccinated patients. The objectives of the current trial were to establish the lowest optimal dose and to confirm the safety of the induction of antibodies against polySA with the NP-polySA vaccine.     

Towards mechanistic models of plant organ growth

Modelling and simulation are increasingly used as tools in the study of plant growth and developmental processes. By formulating experimentally obtained knowledge as a system of interacting mathematical equations, it becomes feasible for biologists to gain a mechanistic understanding of the complex behaviour of biological systems. In this review, the modelling tools that are currently available and the progress that has been made to model plant development, based on experimental knowledge, are described. In terms of implementation, it is argued that, for the modelling of plant organ growth, the cellular level should form the cornerstone. It integrates the output of molecular regulatory networks to two processes, cell division and cell expansion, that drive growth and development of the organ. In turn, these cellular processes are controlled at the molecular level by hormone signalling. Therefore, combining a cellular modelling framework with regulatory modules for the regulation of cell division, expansion, and hormone signalling could form the basis of a functional organ growth simulation model. The current state of progress towards this aim is that the regulation of the cell cycle and hormone transport have been modelled extensively and these modules could be integrated. However, much less progress has been made on the modelling of cell expansion, which urgently needs to be addressed. A limitation of the current generation models is that they are largely qualitative. The possibilities to characterize existing and future models more quantitatively will be discussed. Together with experimental methods to measure crucial model parameters, these modelling techniques provide a basis to develop a Systems Biology approach to gain a fundamental insight into the relationship between gene function and whole organ behaviour.