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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    Publishing for the Protected Area Community: A vision for PARKS from its editorial board
    Amend, T. ; Brooks, T. ; Choudhury, B.C. ; Verschuuren, B. - \ 2014
    PARKS: the International of Protected Areas and Conservation 20 (2014)2. - ISSN 0960-233X - p. 7 - 12.
    In this editorial essay, members of the Editorial Board of PARKS review the status of conservation literature. Three problems are identified: 1) the growing gap between the formal conservation literature and the so-called ‘grey literature’ of project reports, studies and working papers; 2) the effectiveness of the majority of conservation literature in promoting good conservation; and 3) the lack of open access to much of the conservation literature currently available. The article sets out the vision of this journal: PARKS, the International Journal of Protected Areas and Conservation, published by the International Union for Conservation of Nature (IUCN) expert World Commission on Protected Areas (WCPA). PARKS aims to encourage new writers, including younger researchers, conservation professionals who do not generally write for peer-reviewed publications and people from developing countries, including indigenous and local people, to share their best practices in protected area management. PARKS is published twice a year as an online, open-access and peer reviewed journal and welcomes submissions of papers from all protected area professionals worldwide.
    Modeling water potentials and flows in the soil-plant system comparing hydraulic resistances and transpiration reduction fuctions
    Jong, Q. de; Dam, J.C. van; Durigon, A. ; Santos, M.A. dos; Metselaar, K. - \ 2013
    Vadose Zone Journal 12 (2013)3. - ISSN 1539-1663 - 20 p.
    root-water - polymer tensiometers - simulation-model - stress - conductivity - extraction - maize - architecture - transport - movement
    Crop transpiration depends on resistances in the soil–plant–atmosphere system. We present a new deterministic root water uptake model to estimate transpiration and compare it with two other models. We show the sensitivity of actual transpiration to parameters like soil and plant hydraulic properties and root length density distribution with depth. Transpiration reduction functions are often used in hydrological modeling to estimate actual transpiration as a function of soil water status. Empirical reduction functions are most frequently used due to the higher data needs and computational requirements of mechanistic models. Empirical models, however, lack a description of physical mechanisms and their parameters require extensive calibration. We derive a process-based reduction function predicting system potentials, resistances, and water flows. An analytical solution for a special case of Brooks and Corey soils is presented. A numerical version of the reduction function for van Genuchten soils was implemented in the Soil–Water–Atmosphere–Plant (SWAP) hydrological model, allowing predictions for layered soil profiles and root length density variations over depth. The analytical and numerical versions of the model allow an increasingly quantitative insight into the mechanism of root water uptake, such as the existence of a maximum root water uptake rate as a function of soil water status, soil hydraulic properties, root length density, and root radius, in addition to the fact that sensitivity of simulated root water uptake to the radial root conductivity and axial conductance decrease when root length density increases. The approach can be used for the estimation of threshold values for empirical reduction functions.
    International biodiversity offsets
    Peterson, Annah L. ; Hill, Chloe ; Gallagher, Louise A. - \ 2011
    In: Ecosystem Services and Global Trade of Natural Resources / Koellner, Thomas, Taylor and Francis - ISBN 9780415485838 - p. 225 - 241.
    Introduction Intensifying patterns of international trade resulting from globalization create significant challenges for conservation efforts (see Chapter 2 for a more nuanced discussion of the relationship between globalization and conservation). By increasing primary commodity imports (meat, wood, coffee, sugar, etc.), developed nations are indirectly exporting environmental pressures to resource-rich developing countries in the form of heightened land-use change largely manifesting as deforestation and, consequently, increased biodiversity loss (see Chapter 6). Compounding these international drivers of extinction are more local pressures stemming from overpopulation, poverty and a general lack of local incentives for conservation. Together, global and local development pressures have contributed to the growth of the current species extinction rate to between 100 and 1,000 times faster than the historic average (Pimm and Brooks 2000).
    (Flash) Floods on 27 Augustus 2010 in lowland catchments in The Netherlands and Germany
    Brauer, C.C. ; Teuling, A.J. ; Overeem, A. ; Velde, Y. van der; Hazenberg, P. ; Warmerdam, P.M.M. ; Uijlenhoet, R. ; Hobbelt, L.G. - \ 2011
    On 26 August 2010 the eastern part of The Netherlands and the bordering part of Germany were struck by a series of rainfall events. Over an area of 740 km2 more than 120 mm of rainfall were observed in 24 h. This extreme event resulted in local flooding of city centres, highways and agricultural fields, and considerable financial loss. We investigated the unprecedented flash flood triggered by this exceptionally heavy rainfall event in the 6.5 km2 Hupsel Brook catchment, which has been the experimental watershed employed by Wageningen University since the 1960s. This study aims to improve our understanding of the dynamics of such lowland flash floods. We present a detailed hydrometeorological analysis of this extreme event, focusing on its synoptic meteorological characteristics, its space-time rainfall dynamics as observed with rain gauges, weather radar and a microwave link, as well as the measured soil moisture, groundwater and discharge response of the catchment. We found that the response of the Hupsel Brook catchment can be divided into four phases: (1) soil moisture reservoir filling, (2) groundwater response, (3) surface depression filling and surface runoff and (4) backwater feedback. During this extreme event some thresholds became apparent that do not play a role during average conditions and are not incorporated in rainfall-runoff models. Because of the large spatial extent of the rainfall event, many brooks and rivers in the Netherlands and Germany flooded. With data from several catchments we investigated the influence of rainfall and catchment characteristics (such as slope, size and land use) on the reaction of discharge to rainfall.
    Baseline leptin and leptin reduction predict improvements in metabolic variables and long-term fat loss in obese children and adolescents: a prospective study of an inpatient weight-loss program
    Murer, S.B. ; Knopfli, B.H. ; Aeberli, I. ; Jung, A. ; Wildhaber, J. ; Wildhaber-Brooks, J. ; Zimmermann, M.B. - \ 2011
    American Journal of Clinical Nutrition 93 (2011)4. - ISSN 0002-9165 - p. 695 - 702.
    blood-brain-barrier - serum leptin - body-weight - insulin-resistance - loss maintenance - plasma leptin - overweight - adiposity - life - intervention
    Background: It is unclear whether high plasma leptin in obese individuals represents leptin resistance or whether individuals with marked reductions in leptin concentrations in response to weight loss may be at greater risk of regaining weight. Moreover, whether changes in leptin predict metabolic improvements during weight loss is uncertain. Objective: The objective was to prospectively examine associations between plasma leptin, body fat, and weight and metabolic risk factors in obese children during weight loss. Design: In obese children and adolescents [n = 203; mean age: 14.1 y, >98th body mass index (BMI) percentile for age and sex] participating in a 2-mo inpatient weight-loss program, we measured changes in body composition (by dual-energy X-ray absorptiometry), plasma leptin, insulin, and lipids. After discharge, anthropometric measures and plasma leptin were remeasured at 6 (n = 139) and 12 (n = 100) mo. Results: During the 2-mo program, mean (±SD) weight and fat loss were 13.9 ± 4.0 kg and 9.2 ± 2.5 kg, respectively; and mean plasma leptin decreased by 76%. Weight and fat loss were sustained, and no significant differences in BMI-SD score (SDS) or body composition were found between 12 and 2 mo. Baseline leptin was a negative predictor for percentage fat loss at 2, 6, and 12 mo (P <0.05). The percentage change in leptin during the 2-mo intervention positively correlated with the relative change in fasting insulin, the relative change in LDL cholesterol at 2 mo, percentage fat loss, and change in BMI-SDS at 2 and 6 mo (P <0.02). Conclusions: Even in obese children with strongly elevated baseline leptin, large leptin reductions that predict short- and long-term loss of body fat and improvements in lipids and insulin sensitivity can be achieved. Thus, increased plasma leptin in obese children may not necessarily reflect leptin resistance; many children appear to remain leptin sensitive at this age.
    Groundwater recharge in Pleistocene sediments overlying basalt aquifers in the Palouse Basin, USA: modeling of distributed recharge potential and identification of water pathways
    Dijksma, R. ; Brooks, E.S. ; Boll, J. - \ 2011
    Hydrogeology Journal 19 (2011)2. - ISSN 1431-2174 - p. 489 - 500.
    system - tables - smr
    Groundwater levels in basalt aquifers around the world have been declining for many years. Understanding water pathways is needed for solutions like artificial drainage. Water supply in the Palouse Basin, Washington and Idaho, USA, primarily relies on basalt aquifers. This study presents a combination of modeling and field observations to understand the spatial distribution of recharge pathways in the overlying Pleistocene sediments. A spatially distributed model was used to quantify potential recharge rates. The model shows clearly that recharge predominantly occurs through non-argilic soils and soils that are not underlain by fine-grained sediments, i.e. the upper area of the watershed. A field survey was conducted to determine recharge pathways from this area. It revealed 83 perennial springs. Drillings near springs showed connection of coarse-grained layers within the fine-grained Sediments of Bovill to these springs. Such layers, with streambed-like features, act as paleo-channels. Water from one of these coarse-grained layers had a similar electrical conductivity (200 µS cm–1) to water from a downstream perennial spring, also suggesting the existence of a lateral conduit for deep percolation water.
    During Rapid Weight Loss in Obese Children, Reductions in TSH Predict Improvements in Insulin Sensitivity Independent of Changes in Body Weight or Fat
    Aeberli, I. ; Jung, A. ; Murer, S.B. ; Wildhaber, J. ; Wildhaber-Brooks, J. ; Knopfli, B.H. ; Zimmermann, M.B. - \ 2010
    Journal of Clinical Endocrinology and Metabolism 95 (2010)12. - ISSN 0021-972X - p. 5412 - 5418.
    coronary-heart-disease - subclinical hypothyroidism - thyroid-function - reference range - morbid-obesity - in-vivo - leptin - risk - adolescents - population
    Background: Although serum TSH is often elevated in obesity and may be linked to disorders of lipid and glucose metabolism, the clinical relevance of these relationships remains unclear. Subjects: Subjects were obese children and adolescents (n = 206; mean age 14 yr) undergoing rapid weight and fat loss in a standardized, multidisciplinary, 2-month, in-patient weight loss program. Design: This was a prospective study that determined thyroid function, glucose and lipid parameters, leptin, anthropometric measures, and body composition measured by dual-energy x-ray absorption at baseline and at the end of the intervention. Results: At baseline, 52% of children had TSH concentrations in the high normal range (> 2.5 mU/liter), but TSH was not correlated with body weight, body mass index SD scores, lean body mass, or body fat percentage. At baseline, independent of adiposity, TSH significantly correlated with total cholesterol (P = 0.008), low-density lipoprotein cholesterol (P = 0.013), fasting insulin (P = 0.010), homeostatic model assessment (HOMA) (P = 0.004), and leptin (P = 0.006). During the intervention, mean body fat, TSH, HOMA, and fasting insulin decreased by 21, 11, 53, and 54%, respectively. Change (Delta) in TSH did not correlate with Delta body weight or Delta body composition, but Delta TSH significantly correlated with, Delta fasting insulin and Delta HOMA, independent of Delta body weight or Delta body composition (P <0.05). Conclusion: TSH concentrations are elevated in obese children but are not correlated with the amount of excess body weight or fat. During weight loss, independent of changes in body weight or composition, decreases in elevated serum TSH predict decreases in fasting insulin and HOMA. These findings suggest interventions that target high TSH concentrations during weight loss in obese subjects may improve insulin sensitivity. (J Clin Endocrinol Metab 95: 5412-5418, 2010)
    The Bayesian vantage for dealing with uncertainty
    Evans, D. ; Newman, D.J. ; Lavine, M.C. ; Jaworski, J.C. ; Toll, J. ; Brooks, B.W. ; Brock, T.C.M. - \ 2010
    In: Application of uncertainty analysis to ecological risks of pesticides / Warren-Hicks, W.J., Hart, A, Boca Raton, London, New York : SETAC Press & CRC Press, Taylor & Francis Group - ISBN 9781439807347 - p. 71 - 87.
    Historical water management in the river basin of the Baaksche Beek and the adaptations to the water system as a result of change in land use
    Massop, H.T.L. ; Gaast, J.W.J. van der - \ 2009
    Physics and Chemistry of the Earth 34 (2009)3. - ISSN 1474-7065 - p. 192 - 199.
    In the 19th and the first part of the 20th century large parts of the sandy area of The Netherlands were transformed from heath and woodland into agricultural areas. These areas were made suitable for agricultural use by significantly adapting the existing water systems (improving existing brooks, digging new watercourses, etc.). Adaptations will once again be needed, as climate change will increase both precipitation and the peak flow flood waves in the Dutch large rivers. New, pre-emptive adaptations of the current waters system are needed to maintain good agricultural and living conditions, and to prevent catastrophes. Study of the reaction of the water system as a result of previous adaptations is directly relevant to current planning, since such study should reveal the likely long-term outcomes of future adaptations necessitated by climate change
    Voorkom vliegen, voordat je ze ziet vliegen!
    Mul, M.F. ; Brooks, M.D. ; Berg, A.W.H. - \ 2009
    BioKennis bericht Varkensvlees 9 (2009). - 4
    biologische landbouw - varkenshouderij - varkensstallen - diergezondheid - dierenwelzijn - plagenbestrijding - diptera - ziekteoverdracht - bedrijfshygiëne - organic farming - pig farming - pig housing - animal health - animal welfare - pest control - diptera - disease transmission - industrial hygiene
    Vliegen in de stal zijn hinderlijk en kunnen gezondheidsproblemen bij varkens veroorzaken. Wageningen UR Livestock Research heeft het afgelopen jaar de vliegenoverlast en bestrijdingsmethoden geïnventariseerd op biologische varkensbedrijven. Nu is het onderzoek gericht op het voorkomen en weren van vliegen. Dit bioKennisbericht geeft een overzicht van ontwikkelingsplaatsen van vliegen in de stal en tips om vliegenoverlast te voorkomen
    A simple approach to identify critical source areas for phosphorus leaching in the Netherlands
    Salm, C. van der; Schoumans, O.F. ; Walvoort, D.J.J. ; Groenendijk, P. ; Pleijter, M. - \ 2009
    Geophysical Research Abstracts 2009 (2009)11. - ISSN 1029-7006 - p. EGU2009 - 3623.
    High soil phopshorus contents in agricultural soils in the Netherlands cause excessive losses of P to surfacewaters. The reductions in P application rates in the present manure policy are not sufficient to reach surfacewater quality standards resulting from the European Water Framework Directive in all catchments by 2015.Accordingly, additional measures have to be considered to further reduce P loading to surface water. For a costeffective implementation of these measures an instrument to identify critical source areas for phosphorus leachingis indispensable. In the Netherlands phosphorus leaching at a national scale is simulated with a comprehensivemechanistic simulation model (STONE, Wolf et al., 2005) focusing on changes in P leaching with time. Theidentification of critical source areas requires simulations at a high spatial resolution. STONE is less suitable forthis purpose, because of the large number of input parameters required by this complex model. For this reason, asimple model (PLEASE: Phosphorus LEAching from Soils to the Environment; Schoumans et al., in prep.) hasbeen developed based on the same mechanistic process description for inorganic P as the complex model STONEand a simplified description of the lateral flow of water from soil to surface waters. With this model P leachingto surface waters can be calculated using readily available information of field characteristics like depth of thegroundwater table, precipitation surplus and P status and phosphorus adsorption capacity of the soil.To evaluate the performance of the model, it was applied to the Netherlands using the same input as thenational model. Parameterised in this way, PLEASE is a metamodel of STONE. The model was also testedon two small catchments: a catchment with sandy soils and high P accumulation and a clay catchment with amoderate P accumulation. The application at the national scale showed that the overall order of magnitude ofthe calculated leaching fluxes was quite comparable with results of the complex model. However, for individualfields, differences between the two models are sometimes considerable due to differences in the distribution ofthe lateral water fluxes with depth. The application at the catchment scale showed a good agreement betweenmeasured and simulated year average discharge of water and phosphorus. The simulated maps of P leaching forthe two catchments appeared to be plausible with highest P leaching fluxes in intensively used agricultural fieldsin wet areas close to brooks and rivers.Wolf, J. et al. (2005), The integrated modeling system STONE for calculating nutrient emissions fromagriculture in the Netherlands. Environmental Modeling and Software 18, 597-617.Schoumans, O.F., P. Groenendijk and C. van der Salm (in prep.). PLEASE: A simple procedure to determineP losses by leaching
    Assumption 0 analysis: comparative phylogenetic studies in the age of complexity
    Brooks, D.R. ; Veller, M.G.P. van - \ 2008
    Annals of the Missouri Botanical Garden 95 (2008)2. - ISSN 0026-6493 - p. 201 - 223.
    emerging infectious-diseases - a-posteriori methods - vicariance biogeography - historical biogeography - island biogeography - parsimony analysis - cladistic-analysis - contemporary time - area cladograms - species concept
    Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processes
    The shape of the transpiration reduction function under plant water stress
    Metselaar, K. ; Jong van Lier, Q. de - \ 2007
    Vadose Zone Journal 6 (2007)1. - ISSN 1539-1663 - p. 124 - 139.
    bodemwater - bodem-plant relaties - transpiratie - modellen - soil water - soil plant relationships - transpiration - models - available soil-water - leaf-area - balance model - root-system - crop growth - transport - wheat - evaporation - irrigation - responses
    Assuming transpiration to be reduced after a critical pressure head (usually chosen as −1.5 MPa or −150 m) at the root surface has been reached, transpiration rates in this so-called falling-rate phase were analyzed numerically for soils described by the van Genuchten–Mualem equations (numerical soils). The analysis was based on the differential equation describing radial flow to a single root.
    Assuming transpiration to be reduced after a critical pressure head ( usually chosen as -1.5 MPa or -150 m) at the root surface has been reached, transpiration rates in this so-called falling-rate phase were analyzed numerically for soils described by the van Genuchten-Mualem equations ( numerical soils). The analysis was based on the differential equation describing radial flow to a single root. Numerically, the system was simulated by an implicit scheme. It is shown that, at limiting hydraulic conditions, relative transpiration ( ratio between actual and potential transpiration) is equal to relative matric flux potential ( ratio between actual matric flux potential and matric flux potential at the onset of limiting hydraulic conditions). Given this equality, transpiration reduction functions as a function of soil water content and as a function of time are presented for five types of analytical soils: a constant diffusivity, Green and Ampt, Brooks and Corey, versatile nonlinear, and exponential soil. While in the case of constant diffusivity, relative transpiration decreases as a linear function of water content, for the remaining four cases the decrease is a concave function of soil water content. Numerical simulations also result in a concave shape, unless the difference between water content at the onset of limiting hydraulic conditions and at permanent wilting is very small, for example, at high root densities. These discrepancies may be explained by the relative importance of a transition period between the constant- and falling-rate phases.
    Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands
    Bezemer, T.M. ; Lawson, C.S. ; Hedlund, K. ; Edwards, A.R. ; Brooks, A.J. ; Igual, J.M. ; Mortimer, S.R. ; Putten, W.H. van der - \ 2006
    Journal of Ecology 94 (2006)5. - ISSN 0022-0477 - p. 893 - 904.
    fatty-acid analysis - community structure - diversity - rhizosphere - vegetation - biota - dynamics - biomass - succession - management
    1 Plant species differ in their capacity to influence soil organic matter, soil nutrient availability and the composition of soil microbial communities. Their influences on soil properties result in net positive or negative feedback effects, which influence plant performance and plant community composition. 2 For two grassland systems, one on a sandy soil in the Netherlands and one on a chalk soil in the United Kingdom, we investigated how individual plant species grown in monocultures changed abiotic and biotic soil conditions. Then, we determined feedback effects of these soils to plants of the same or different species. Feedback effects were analysed at the level of plant species and plant taxonomic groups (grasses vs. forbs). 3 In the sandy soils, plant species differed in their effects on soil chemical properties, in particular potassium levels, but PLFA (phospholipid fatty acid) signatures of the soil microbial community did not differ between plant species. The effects of soil chemical properties were even greater when grasses and forbs were compared, especially because potassium levels were lower in grass monocultures. 4 In the chalk soil, there were no effects of plant species on soil chemical properties, but PLFA profiles differed significantly between soils from different monocultures. PLFA profiles differed between species, rather than between grasses and forbs. 5 In the feedback experiment, all plant species in sandy soils grew less vigorously in soils conditioned by grasses than in soils conditioned by forbs. These effects correlated significantly with soil chemical properties. None of the seven plant species showed significant differences between performance in soil conditioned by the same vs. other plant species. 6 In the chalk soil, Sanguisorba minor and in particular Briza media performed best in soil collected from conspecifics, while Bromus erectus performed best in soil from heterospecifics. There was no distinctive pattern between soils collected from forb and grass monocultures, and plant performance could not be related to soil chemical properties or PLFA signatures. 7 Our study shows that mechanisms of plant-soil feedback can depend on plant species, plant taxonomic (or functional) groups and site-specific differences in abiotic and biotic soil properties. Understanding how plant species can influence their rhizosphere, and how other plant species respond to these changes, will greatly enhance our understanding of the functioning and stability of ecosystems.
    Fermentation of wheat: effects of backslopping different proportions of pre-fermented wheat on the microbial and chemical composition
    Moran, C.A. ; Scholten, R.H.J. ; Tricarico, J.M. ; Brooks, P.H. ; Verstegen, M.W.A. - \ 2006
    Archives of Animal Nutrition 60 (2006)2. - ISSN 1745-039X - p. 158 - 169.
    liquid compound diets - 6-day storage period - fed ad-libitum - organic-acids - coproducts - feed - pigs - performance - food
    The objective of the study was to examine effect of backslop on the chemical and microbiological characteristics of fermented wheat (FW). Coarsely ground wheat was mixed with water (1:3 wt/wt) and inoculated with 6 log cfu ml(-1) each of an overnight culture of Lactobacillus plantarum and Pediococcus pentosaceus. Four fermentation treatments were conducted in 45 1, closed, PVC containers over 48 hours. Three treatments investigated the benefits of the addition of previously fermented wheat (backslopping, BSL) at different proportions (0.20, 0.33 or 0.42 kg) to freshly prepared wheat. The control treatment contained no addition of BSL. Elimination of coliforms from the FW within 48 h was only achieved through backslopping; where coliform bacteria counts decreased from approximately 6.5 log10 cfu ml(-1) to less than 3 log10 cfu ml(-1). There was no apparent advantage in increasing the backslop proportion above 0.20. However, the exclusion of coliform bacteria required the pH to remain below 4.0 for at a minimum of 24 h. The results of these studies indicate that fermentation of wheat has the potential to reduce the risk of feed-borne colibacillosis and provides a practical alternative to producers that cannot ferment multiple diets or have limited fermentation capacity.
    Inter-laboratory variation in in vitro gas production profiles of some selected feeds, using both manual and automated methods
    Rymer, C. ; Williams, B.A. ; Brooks, A.E. ; Davies, D.R. ; Givens, D.I. - \ 2005
    Animal Feed Science and Technology 123-124 (2005)1. - ISSN 0377-8401 - p. 225 - 241.
    temperature dried grass - neutral detergent fiber - fatty-acid production - fermentation kinetics - ruminant feeds - rumen fluid - pressure transducer - forages - degradability - degradation
    A study was conducted to estimate variation among laboratories and between manual and automated techniques of measuring pressure on the resulting gas production profiles (GPP). Eight feeds (molassed sugarbeet feed, grass silage, maize silage, soyabean hulls, maize gluten feed, whole crop wheat silage, wheat, glucose) were milled to pass a 1 mm screen and sent to three laboratories (ADAS Nutritional Sciences Research Unit, UK; Institute of Grassland and Environmental Research (IGER), UK; Wageningen University, The Netherlands). Each laboratory measured GPP over 144 h using standardised procedures with manual pressure transducers (MPT) and automated pressure systems (APS). The APS at ADAS used a pressure transducer and bottles in a shaking water bath, while the APS at Wageningen and IGER used a pressure sensor and bottles held in a stationary rack. Apparent dry matter degradability (ADDM) was estimated at the end of the incubation. GPP were fitted to a modified Michaelis¿Menten model assuming a single phase of gas production, and GPP were described in terms of the asymptotic volume of gas produced (A), the time to half A (B), the time of maximum gas production rate (tRM gas) and maximum gas production rate (RM gas). There were effects (P
    An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm
    Armstrong, R. ; Whisson, S.C. ; Pritchard, L. ; Bos, J.I.B. ; Venter, E. ; Avrova, A.O. ; Rehmany, A.P. ; Bohme, U. ; Brooks, K. ; Cherevach, I. ; Hamlin, N. ; White, B. ; Fraser, A. ; Lord, A. ; Quail, M.A. ; Churcher, C. ; Hall, N. ; Berriman, M. ; Huang, S. ; Kamoun, S. ; Beynon, J.L. ; Birch, P.R.J. - \ 2005
    Proceedings of the National Academy of Sciences of the United States of America 102 (2005)21. - ISSN 0027-8424 - p. 7766 - 7771.
    phytophthora-infestans - comparative genomics - disease resistance - potato famine - plant-cells - arabidopsis - evolution - products - elicitor - fungus
    Plants sense phosphate (Pi) deficiency and initiate signaling that controls adaptive responses necessary for Pi acquisition. Herein, evidence establishes that AtSIZ1 is a plant small ubiquitin-like modifier (SUMO) E3 ligase and is a focal controller of Pi starvation-dependent responses. T-DNA insertional mutated alleles of AtSIZ1 (At5g60410) cause Arabidopsis to exhibit exaggerated prototypical Pi starvation responses, including cessation of primary root growth, extensive lateral root and root hair development, increase in root/shoot mass ratio, and greater anthocyanin accumulation, even though intracellular Pi levels in siz1 plants were similar to wild type. AtSIZ1 has SUMO E3 ligase activity in vitro, and immunoblot analysis revealed that the protein sumoylation profile is impaired in siz1 plants. AtSIZ1-GFP was localized to nuclear foci. Steadystate transcript abundances of Pi starvation-responsive genes AtPT2, AtPS2, and AtPS3 were moderate but clearly greater in siz1 seedlings than in wild type, where Pi is sufficient. Pi starvation induced the expression of these genes to the same extent in siz1 and wild-type seedlings. However, two other Pi starvation-responsive genes, AtIPS1 and AtRNS1, are induced more slowly in siz1 seedlings by Pi limitation. PHR1, a MYB transcriptional activator of AtIPS1 and AtRNS1, is an AtSIZ1 sumoylation target. These results indicate that AtSIZ1 is a SUMO E3 ligase and that sumoylation is a control mechanism that acts both negatively and positively on different Pi deficiency responses
    Tight coupling between leaf area index and foliage N content in arctic plant communities
    Wijk, M.T. van; Williams, M. ; Shaver, G.R. - \ 2005
    Oecologia 142 (2005)3. - ISSN 0029-8549 - p. 421 - 427.
    brooks-range-foothills - tundra ecosystems - northern alaska - tussock tundra - responses - biomass - productivity - toposequence - vegetation - landscape
    The large spatial heterogeneity of arctic landscapes complicates efforts to quantify key processes of these ecosystems, for example productivity, at the landscape level. Robust relationships that help to simplify and explain observed patterns, are thus powerful tools for understanding and predicting vegetation distribution and dynamics. Here we present the same linear relationship between Leaf area index (LAI) and Total foliar nitrogen (TFN), the two factors determining the photosynthetic capacity of vegetation, across a wide range of tundra vegetation types in both northern Sweden and Alaska between leaf area indices of 0 and 1 m(2) m(-2), which is essentially the entire range of leaf area index values for the Arctic as a whole. Surprisingly, this simple relationship arises as an emergent property at the plant community level, whereas at the species level a large variability in leaf traits exists. As the relationship between LAI and TFN exists among such varied ecosystems, the arctic environment must impose tight constraints on vegetation canopy development. This relationship simplifies the quantification of vegetation productivity of arctic vegetation types as the two most important drivers of productivity can be estimated reliably from remotely sensed NDVI images.
    Report on the infauna sampling by TDI Brooks. Visit to Nigeria June 27th until June 30th 2004
    Boois, I.J. de - \ 2004
    IJmuiden : RIVO (Report C060/04) - 12 p.
    Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story
    Brooks, D.R. ; Dowling, A.P.G. ; Veller, M.G.P. van; Hoberg, E.P. - \ 2004
    Cladistics-The International Journal of the Willi Hennig Society 20 (2004)1. - ISSN 0748-3007 - p. 32 - 46.
    brooks parsimony analysis - host-parasite coevolution - a-posteriori methods - historical biogeography - vicariance biogeography - cladistic biogeography - phylogenetic biogeography - associations - assumptions - speciation
    Prior studies involving two methods, Brooks Parsimony Analysis (BPA) and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offered new exemplars to demonstrate flaws in BPA, plus a simple fix to correct the flaws found in TreeMap. A re-evaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographic studies
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