Showing papers by "Wageningen University and Research Centre published in 2005"

Determinants of woody cover in African savannas

Abstract: Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties1–3. The availability of resources (water, nutrients) and disturbance regimes (fire, herbivory) are thought to be important in regulating woody cover1,2,4,5, but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than ,650mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered ‘stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP-controlled upper bound. Above a MAP of ,650mm, savannas are ‘unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances (fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation6 may considerably affect their distribution and dynamics.

Extensive sorption of organic compounds to black carbon, coal, and kerogen in sediments and soils: mechanisms and consequences for distribution, bioaccumulation, and biodegradation

Abstract: Evidence is accumulating that sorption of organic chemicals to soils and sediments can be described by “dual-mode sorption”: absorption in amorphous organic matter (AOM) and adsorption to carbonaceous materials such as black carbon (BC), coal, and kerogen, collectively termed “carbonaceous geosorbents” (CG). Median BC contents as a fraction of total organic carbon are 9% for sediments (number of sediments, n ≈ 300) and 4% for soils (n = 90). Adsorption of organic compounds to CG is nonlinear and generally exceeds absorption in AOM by a factor of 10−100. Sorption to CG is particularly extensive for organic compounds that can attain a more planar molecular configuration. The CG adsorption domain probably consists of surface sites and nanopores. In this review it is shown that nonlinear sorption to CG can completely dominate total sorption at low aqueous concentrations (<10-6 of maximum solid solubility). Therefore, the presence of CG can explain (i) sorption to soils and sediments being up to 2 orders of m...

Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack.

Abstract: 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), tissuechewing 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 P. 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.

Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products

Abstract: Flavour development in dairy fermentations, most notably cheeses, results from a series of (bio)chemical processes in which the starter cultures provide the enzymes. Particularly the enzymatic degradation of proteins (caseins) leads to the formation of key-flavour components, which contribute to the sensory perception of dairy products. More specifically, caseins are degraded into peptides and amino acids and the latter are major precursors for volatile aroma compounds. In particular, the conversion of methionine, the aromatic and the branched-chain amino acids are crucial. A lot of research has focused on the degradation of caseins into peptides and free amino acids, and more recently, enzymes involved in the conversion of amino acids were identified. Most data are generated on Lactococcus lactis, which is the predominant organism in starter cultures used for cheese-making, but also Lactobacillus, Streptococcus, Propionibacterium and species used for surface ripening of cheeses are characterised in their flavour-forming capacity. In this paper, various enzymes and pathways involved in flavour formation will be highlighted and the impact of these findings for the development of industrial starter cultures will be discussed.

Future Directions of Precision Agriculture

Abstract: Precision Agriculture is advancing but not as fast as predicted 5 years ago. The development of proper decision-support systems for implementing precision decisions remains a major stumbling block to adoption. Other critical research issues are discussed, namely, insufficient recognition of temporal variation, lack of whole-farm focus, crop quality assessment methods, product tracking and environmental auditing. A generic research programme for precision agriculture is presented. A typology of agriculture countries is introduced and the potential of each type for precision agriculture discussed.

A climatic stratification of the environment of Europe

Abstract: Aim To produce a statistical stratification of the European environment, suitable for stratified random sampling of ecological resources, the selection of sites for representative studies across the continent, and to provide strata for modelling exercises and reporting. Location A ‘Greater European Window’ with the following boundaries: 11 ° W, 32 ° E, 34 ° N, 72 ° N. Methods Tw enty of the most relevant available environmental variables were selected, based on experience from previous studies. Principal components analysis (PCA) was used to explain 88% of the variation into three dimensions, which were subsequently clustered using an ISODATA clustering routine. The mean first principal component values of the classification variables were used to aggregate the strata into Environmental Zones and to provide a basis for consistent nomenclature. Results The Environmental Stratification of Europe (EnS) consists of 84 strata, which have been aggregated into 13 Environmental Zones. The stratification has a 1 km 2 resolution. Aggregations of the strata have been compared to other European classifications using the Kappa statistic, and show ‘good’ comparisons. The individual strata have been described using data from available environmental databases. The EnS is available for noncommercial use by applying to the corresponding author. Main conclusions The Environmental Stratification of Europe has been constructed using tried and tested statistical procedures. It forms an appropriate stratification for stratified random sampling of ecological resources, the selection of sites for representative studies across the continent and for the provision of strata for modelling exercises and reporting at the European scale.

Sources and delivery of carbon, nitrogen, and phosphorus to the coastal zone : An overview of global nutrient export from watersheds (NEWS) models and their application

Abstract: [1] An overview of the first spatially explicit, multielement (N, P, and C), multiform (dissolved inorganic: DIN, DIP; dissolved organic: DOC, DON, DOP; and particulate: POC, PN, PP) predictive model system of river nutrient export from watersheds (Global Nutrient Export from Watersheds (NEWS)) is presented. NEWS models estimate export from 5761 watersheds globally as a function of land use, nutrient inputs, hydrology, and other factors; regional and global scale patterns as of 1995 are presented here. Watershed sources and their relative magnitudes differ by element and form. For example, anthropogenic sources dominate the export of DIN and DIP at the global scale, although their anthropogenic sources differ significantly (diffuse and point, respectively). Natural sources dominate DON and DOP export globally, although diffuse anthropogenic sources dominate in several regions in Asia, Europe and N. America. “Hot spots” where yield (kg km−2 yr−1) is high for several elements and forms were identified, including parts of Indonesia, Japan, southern Asia, and Central America, due to anthropogenic N and P inputs in some regions and high water runoff in others. NEWS models provide a tool to examine past, current and future river export of nutrients, and how humans might impact element ratios and forms, and thereby affect estuaries and coastal seas.

Species divergence and trait convergence in experimental plant community assembly

Abstract: Despite decades of research, it remains controversial whether ecological communities converge towards a common structure determined by environmental conditions irrespective of assembly history. Here, we show experimentally that the answer depends on the level of community organization considered. In a 9-year grassland experiment, we manipulated initial plant composition on abandoned arable land and subsequently allowed natural colonization. Initial compositional variation caused plant communities to remain divergent in species identities, even though these same communities converged strongly in species traits. This contrast between species divergence and trait convergence could not be explained by dispersal limitation or community neutrality alone. Our results show that the simultaneous operation of trait-based assembly rules and species-level priority effects drives community assembly, making it both deterministic and historically contingent, but at different levels of community organization.

The strigolactone germination stimulants of the plant-parasitic Striga and Orobanche spp. are derived from the carotenoid pathway

Abstract: The seeds of parasitic plants of the genera Striga and Orobanche will only germinate after induction by a chemical signal exuded from the roots of their host. Up to now, several of these germination stimulants have been isolated and identified in the root exudates of a series of host plants of both Orobanche and Striga spp. In most cases, the compounds were shown to be isoprenoid and belong to one chemical class, collectively called the strigolactones, and suggested by many authors to be sesquiterpene lactones. However, this classification was never proven; hence, the biosynthetic pathways of the germination stimulants are unknown. We have used carotenoid mutants of maize (Zea mays) and inhibitors of isoprenoid pathways on maize, cowpea (Vigna unguiculata), and sorghum (Sorghum bicolor) and assessed the effects on the root exudate-induced germination of Striga hermonthica and Orobanche crenata. Here, we show that for these three host and two parasitic plant species, the strigolactone germination stimulants are derived from the carotenoid pathway. Furthermore, we hypothesize how the germination stimulants are formed. We also discuss this finding as an explanation for some phenomena that have been observed for the host-parasitic plant interaction, such as the effect of mycorrhiza on S. hermonthica infestation.

Molecular basis of photoprotection and control of photosynthetic light-harvesting

Abstract: In order to maximize their use of light energy in photosynthesis, plants have molecules that act as light-harvesting antennae, which collect light quanta and deliver them to the reaction centres, where energy conversion into a chemical form takes place. The functioning of the antenna responds to the extreme changes in the intensity of sunlight encountered in nature. In shade, light is efficiently harvested in photosynthesis. However, in full sunlight, much of the energy absorbed is not needed and there are vitally important switches to specific antenna states, which safely dissipate the excess energy as heat. This is essential for plant survival, because it provides protection against the potential photo-damage of the photosynthetic membrane. But whereas the features that establish high photosynthetic efficiency have been highlighted, almost nothing is known about the molecular nature of the dissipative states. Recently, the atomic structure of the major plant light-harvesting antenna protein, LHCII, has been determined by X-ray crystallography. Here we demonstrate that this is the structure of a dissipative state of LHCII. We present a spectroscopic analysis of this crystal form, and identify the specific changes in configuration of its pigment population that give LHCII the intrinsic capability to regulate energy flow. This provides a molecular basis for understanding the control of photosynthetic light-harvesting.

Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors

Abstract: Interactions between proteins are essential for their functioning and the biological processes they control. The elucidation of interaction maps based on yeast studies is a first step toward the understanding of molecular networks and provides a framework of proteins that possess the capacity and specificity to interact. Here, we present a comprehensive plant protein–protein interactome map of nearly all members of the Arabidopsis thaliana MADS box transcription factor family. A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers. Clustering of proteins with similar interaction patterns pinpoints proteins involved in the same developmental program and provides valuable information about the participation of uncharacterized proteins in these programs. Furthermore, a model is proposed that integrates the floral induction and floral organ formation networks based on the interactions between the proteins involved. Heterodimers between flower induction and floral organ identity proteins were observed, which point to (auto)regulatory mechanisms that prevent the activity of flower induction proteins in the flower.

Linking aboveground and belowground interactions via induced plant defenses

Abstract: Plants have a variety of chemical defenses that often increase in concentration following attack by herbivores. Such induced plant responses can occur aboveground, in the leaves, and also belowground in the roots. We show here that belowground organisms can also induce defense responses aboveground and vice versa. Indirect defenses are particularly sensitive to interference by induced feeding activities in the other compartment, and this can disrupt multitrophic interactions. Unravelling the involvement of induced plant responses in the interactions between aboveground and belowground communities associated with plants is likely to benefit from comprehensive metabolomic analyses. Such analyses are likely to contribute to a better understanding of the costs and benefits involved in the selection for induced responses in plants.

Genetic engineering of terpenoid metabolism attracts bodyguards to Arabidopsis.

Abstract: Herbivore-damaged plants release complex mixtures of volatiles that attract natural enemies of the herbivore. To study the relevance of individual components of these mixtures for predator attraction, we manipulated herbivory-induced volatiles through genetic engineering. Metabolic engineering of terpenoids, which dominate the composition of many induced plant volatile bouquets, holds particular promise. By switching the subcellular localization of the introduced sesquiterpene synthase to the mitochondria, we obtained transgenic Arabidopsis thaliana plants emitting two new isoprenoids. These altered plants attracted carnivorous predatory mites (Phytoseiulus persimilis) that aid the plants' defense mechanisms.

Measuring Eco-efficiency of Production with Data Envelopment Analysis

Abstract: Summary Aggregation of environmental pressures into a single environmental damage index is a major challenge of eco-efficiency measurement. This article examines how the data envelopment analysis (DEA) method can be adapted for this purpose. DEA accounts for substitution possibilities between different natural resources and emissions and does not require subjective judgment about the weights. Although DEA does not require subjective or normative judgment, soft weight restrictions can be incorporated into the framework. The proposed approach is illustrated by an application to assessing ecoefficiency of road transportation in the three largest towns of eastern Finland.

Measurement and Interpretation of Electrokinetic Phenomena (IUPAC Technical Report)

Abstract: In this report, the status quo and recent progress in electrokinetics are reviewed. Practical rules are recommended for performing electrokinetic measurements and interpreting their results in terms of well-defined quantities, the most familiar being the ?-potential or electrokinetic potential. This potential is a property of charged interfaces, and it should be independent of the technique used for its determination. However, often the ?-potential is not the only property electrokinetically characterizing the electrical state of the interfacial region: the excess conductivity of the stagnant layer is an additional parameter. The requirement to obtain the ?-potential is that electrokinetic theories be correctly used and applied within their range of validity. Basic theories and their application ranges are discussed. A thorough description of the main electrokinetic methods is given: special attention is paid to their ranges of applicability as well as to the validity of the underlying theoretical models. Electrokinetic consistency tests are proposed in order to assess the validity of the ?-potentials obtained. The recommendations given in the report apply mainly to smooth and homogeneous solid particles and plugs in aqueous systems; some attention is paid to nonaqueous media and less ideal surfaces

Cladosporium Avr2 inhibits tomato Rcr3 protease required for Cf-2-dependent disease resistance.

Abstract: How plants recognize pathogens and activate defense is still mysterious. Direct interaction between pathogen avirulence (Avr) proteins and plant disease resistance proteins is the exception rather than the rule. During infection, Cladosporium fulvum secretes Avr2 protein into the apoplast of tomato leaves and, in the presence of the extracellular leucine-rich repeat receptor-like Cf-2 protein, triggers a hypersensitive response (HR) that also requires the extracellular tomato cysteine protease Rcr3. We show here that Avr2 binds and inhibits Rcr3 and propose that the Rcr3-Avr2 complex enables the Cf-2 protein to activate an HR.

Tissue Distribution of Quercetin in Rats and Pigs

Abstract: Quercetin is a dietary polyphenolic compound with potentially beneficial effects on health. Claims that quercetin has biological effects are based mainly on in vitro studies with quercetin aglycone. However, quercetin is rapidly metabolized, and we have little knowledge of its availability to tissues. To assess the long-term tissue distribution of quercetin, 2 groups of rats were given a 0.1 or 1% quercetin diet [∼50 or 500 mg/kg body weight (wt)] for 11 wk. In addition, a 3-d study was done with pigs fed a diet containing 500 mg quercetin/kg body wt. Tissue concentrations of quercetin and quercetin metabolites were analyzed with an optimized extraction method. Quercetin and quercetin metabolites were widely distributed in rat tissues, with the highest concentrations in lungs (3.98 and 15.3 nmol/g tissue for the 0.1 and 1% quercetin diet, respectively) and the lowest in brain, white fat, and spleen. In the short-term pig study, liver (5.87 nmol/g tissue) and kidney (2.51 nmol/g tissue) contained high concentrations of quercetin and quercetin metabolites, whereas brain, heart, and spleen had low concentrations. These studies have for the first time identified target tissues of quercetin, which may help to understand its mechanisms of action in vivo. © 2005 American Society for Nutritional Sciences.

Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes

Abstract: Tomatoes are a principal dietary source of carotenoids and flavonoids, both of which are highly beneficial for human health. Overexpression of genes encoding biosynthetic enzymes or transcription factors have resulted in tomatoes with improved carotenoid or flavonoid content, but never with both. We attempted to increase tomato fruit nutritional value by suppressing an endogenous photomorphogenesis regulatory gene, DET1, using fruit-specific promoters combined with RNA interference (RNAi) technology. Molecular analysis indicated that DET1 transcripts were indeed specifically degraded in transgenic fruits. Both carotenoid and flavonoid contents were increased significantly, whereas other parameters of fruit quality were largely unchanged. These results demonstrate that manipulation of a plant regulatory gene can simultaneously influence the production of several phytonutrients generated from independent biosynthetic pathways, and provide a novel example of the use of organ-specific gene silencing to improve the nutritional value of plant-derived products.

An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm

Abstract: The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847. It represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. Nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. Disease resistance alleles, products of which recognize corresponding avirulence molecules in the pathogen, have been introgressed into the cultivated potato from a wild species, Solanum demissum, and R1 and R3a have been identified. We used association genetics to identify Avr3a and show that it encodes a protein that is recognized in the host cytoplasm, where it triggers R3a-dependent cell death. Avr3a resides in a region of the P. infestans genome that is colinear with the locus containing avirulence gene ATR1NdWsB in Hyaloperonospora parasitica, an oomycete pathogen of Arabidopsis. Remarkably, distances between conserved genes in these avirulence loci were often similar, despite intervening genomic variation. We suggest that Avr3a has undergone gene duplication and that an allele evading recognition by R3a arose under positive selection.

Lignan contents of Dutch plant foods: a database including lariciresinol, pinoresinol, secoisolariciresinol and matairesinol.

Abstract: Enterolignans ( enterodiol and enterolactone) can potentially reduce the risk of certain cancers and cardiovascular diseases. Enterolignans are formed by the intestinal microflora after the consumption of plant lignans. Until recently, only secoisolariciresinol and matairesinol were considered enterolignan precursors, but now several new precursors have been identified, of which lariciresinol and pinoresinol have a high degree of conversion. Quantitative data on the contents in foods of these new enterolignan precursors are not available. Thus, the aim of this study was to compile a lignan database including all four major enterolignan precursors. Liquid chromatography-tandem mass spectrometry was used to quantify lariciresinol, pinoresinol, secoisolariciresinol and matairesinol in eighty-three solid foods and twenty-six beverages commonly consumed in The Netherlands. The richest source of lignans was flaxseed (301 129 μ g/100 g), which contained mainly secoisolariciresinol. Also, lignan concentrations in sesame seeds (29 331 μ g/100 g, mainly pinoresinol and lariciresinol) were relatively high. For grain products, which are known to be important sources of lignan, lignan concentrations ranged from 7 to 764 μ g/100 g. However, many vegetables and fruits had similar concentrations, because of the contribution of lariciresinol and pinoresinol. Brassica vegetables contained unexpectedly high levels of lignans (185-2321 μ g/100 g), mainly pinoresinol and lariciresinol. Lignan levels in beverages varied from 0 (cola) to 91 μ g/100 ml (red wine). Only four of the 109 foods did not contain a measurable amount of lignans, and in most cases the amount of lariciresinol and pinoresinol was larger than that of secoisolariciresinol and matairesinol. Thus, available databases largely underestimate the amount of enterolignan precursors in foods.

Benefits and uses of urban forests and trees

Abstract: Trees and forests are, because of seasonal changes and their size, shape, and color, the most prominent elements of urban nature. Their benefits and uses range from intangible psychological and aesthetic benefits to amelioration of urban climate and mitigation of air pollution. Historically the main benefits of urban trees and forests relate to health, aesthetic and recreational benefits in industrialized cities. Moreover, green areas have provided people with subsistence by providing food, fodder, fuel, wood and timber for construction (see Chap. 2). Today, woodland, woods and trees are important to people especially through symbolizing personal, local, community and cultural meanings. They provide aesthetic enjoyment and create a pleasant environment for different outdoor activities. Woodland can provide an experience of nature in the middle of urban life. In particular, old woodland with big trees may provide urban people with the opportunity to recover from daily stress, revive memories and regain confidence. There is also an important educational value of urban forests. Contact with trees, in particular for children, can help people learn about nature and natural processes in an otherwise artificial environment. Urban trees and woodland also contribute to an attractive green townscape and thus communicate the image of a positive, nature-oriented city. Indirectly, urban trees and forests can promote tourism and enhance economic development. At the local level trees contribute to the quality of housing and working environments and their benefits are reflected in property values. The same urban woodland areas and trees may have multiple benefits that reinforce each other. Recreational woodland, for example, also reduces wind speed and traffic noise as well as improves the landscape in a nearby residential area. To a certain extent the distinction between different categories of benefits is artificial. However benefits have their own special features and therefore can be presented separately (Table 4.1). While these benefits of urban woodland, other tree stands and individual trees are not new they are still insufficiently recognised in urban planning and development processes (see Chap. 5). There is need to provide more knowledge on the role of urban woodland and trees in improvement of the environment and relate this to their social functions such as fostering mental and physical health. This chapter aims to give insight into the current state of knowledge about benefits and uses of urban forests and trees in Europe. This is a difficult enterprise due to the complexity of the European continent. Urban forest research is largely national or even Benefits and Uses of Urban Forests and Trees

Significance testing of synergistic/antagonistic, dose level‐dependent, or dose ratio‐dependent effects in mixture dose‐response analysis

Abstract: In ecotoxicology, the state of the art for effect assessment of chemical mixtures is through multiple dose-response analysis of single compounds and their combinations. Investigating whether such data deviate from the reference models of concentration addition and/or independent action to identify overall synergism or antagonism is becoming routine. However, recent data show that more complex deviation patterns, such as dose ratio-dependent deviation and dose level-dependent deviation, need to be addressed. For concentration addition, methods to detect such deviation patterns exist, but they are stand-alone methods developed separately in literature, and conclusions derived from these analyses are therefore difficult to compare. For independent action, hardly any methods to detect such deviations from this reference model exist. This paper describes how these well-established mixture toxicity principles have been incorporated in a coherent data analysis procedure enabling detection and quantification of dose level-and dose ratio-specific synergism or antagonism from both the concentration addition and the independent action models. Significance testing of which deviation pattern describes the data best is carried out through maximum likelihood analysis. This analysis procedure is demonstrated through various data sets, and its applicability and limitations in mixture research are discussed.