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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Phenotypic trait variation measured on european genetic trials of fagus sylvatica L
Robson, Matthew T. ; Garzón, Marta Benito ; Miranda, Ricardo Alia ; Egido, Diana Barba ; Bogdan, Saša ; Borovics, Attila ; Božič, Gregor ; Brendel, Oliver ; Clark, Jo ; Vries, Sven M.G. de; Delehan, Ivan I. ; Ducousso, Alexis ; Fady, Bruno ; Fennessy, John ; Forstreuter, Manfred ; Frýdl, Josef ; Geburek, Thomas ; Gömöry, Dušan ; Hauke-Kowalska, Maria ; Huber, Gerhard ; Ibañez, Juan Ignacio ; Ioniţă, Lucia ; Ivankovič, Mladen ; Hansen, Jon Kehlet ; Kóczán-Horváth, Anikó ; Kraigher, Hojka ; Lee, Steve ; Liesebach, Mirko ; Mátyás, Csaba ; Mertens, Patrick ; Muhs, Hans Jakob ; Novotný, Petr ; Parnuţa, Gheorghe ; Paule, Ladislav ; Picardo, Alvaro ; Rasztovics, Ervin ; Rogge, Martin ; Stener, Lars Göran ; Sułkowska, Małgorzata ; Urban, Otmar ; Wuehlisch, Georg Von; Vendramin, Giovanni G. ; Vettori, Cristina ; Wesoły, Wojciech - \ 2018
Scientific Data 5 (2018). - ISSN 2052-4463
We present BeechCOSTe52; a database of European beech (Fagus sylvatica) phenotypic measurements for several traits related to fitness measured in genetic trials planted across Europe. The dataset was compiled and harmonized during the COST-Action E52 (2006-2010), and subsequently cross-validated to ensure consistency of measurement data among trials and provenances. Phenotypic traits (height, diameter at breast height, basal diameter, mortality, phenology of spring bud burst and autumn-leaf discoloration) were recorded in 38 trial sites where 217 provenances covering the entire distribution of European beech were established in two consecutive series (1993/95 and 1996/98). The recorded data refer to 862,095 measurements of the same trees aged from 2 to 15 years old over multiple years. This dataset captures the considerable genetic and phenotypic intra-specific variation present in European beech and should be of interest to researchers from several disciplines including quantitative genetics, ecology, biogeography, macroecology, adaptive management of forests and bioeconomy.
Re-thinking the politics of migration. On the uses and challenges of regime perspectives for migration research
Horvath, Kenneth ; Amelinaz, Anna ; Peters, Karin - \ 2017
Migration Studies 5 (2017)3. - ISSN 2049-5838 - p. 301 - 314.
Borders - Europe - Migration politics - Migration regimes - Mobilities - Regime theory
The aim of this special issue is to critically assess the potential of regime theory for migration research. Against the background of contemporary political dynamics, regime terminology has become rather popular in migration studies. There has, however, been little debate on the foundations and implications of the very notion of 'regime'. Although regime is anything but a unified concept, in this article we argue that there are commonalities in analytical perspectives useful for migration research. Current usages in migration research are informed by at least four different strands of theory building that differ in their epistemological, ontological, and methodological foundations: (i) international relations-notions of regimes as international regulatory frameworks, (ii) conceptualizations informed by welfare regime theories, (iii) regime notions that stem from the French regulation school, and (iv) regime theories inspired by governmentality studies. The collection of articles in this special issue mirrors this constellation. The contributions come from different disciplinary and methodological backgrounds, employ different regime notions, and focus on a wide range of aspects of contemporary European migration politics. While it seems crucial to acknowledge this conceptual variety, we argue that there are also important points of convergence between these strands of theory building: attention to the complexities and contradictions of regulatory practices, a focus on normative and discursive orders, and consideration of relations of power and inequality. This specific simultaneity of variety and convergence may open spaces for academic debates that move beyond established conceptual and methodological boundaries.
Scientific opinion: Risks for public health related to the presence of tetrodotoxin (TTX) and TTX analogues in marine bivalves and gastropods
Knutsen, Helle Katrine ; Alexander, Jan ; Barregård, Lars ; Bignami, Margherita ; Brüschweiler, Beat ; Ceccatelli, Sandra ; Cottrill, Bruce ; Dinovi, Michael ; Edler, Lutz ; Grasl-Kraupp, Bettina ; Hogstrand, Christer ; Hoogenboom, L.A.P. ; Nebbia, Carlo Stefano ; Oswald, Isabelle P. ; Rose, Martin ; Roudot, Alain-Claude ; Schwerdtle, Tanja ; Vleminckx, Christiane ; Vollmer, Günter ; Wallace, Heather ; Arnich, Nathalie ; Benford, Diane ; Botana, Luis ; Viviani, Barbara ; Arcella, Davide ; Binaglia, Marco ; Horvath, Zsuzsanna ; Steinkellner, Hans ; Manen, Mathijs Van; Petersen, Annette - \ 2017
EFSA Journal 15 (2017)4. - ISSN 1831-4732
Tetrodotoxin (TTX) and its analogues are produced by marine bacteria and have been detected in marine bivalves and gastropods from European waters. The European Commission asked EFSA for a scientific opinion on the risks to public health related to the presence of TTX and TTX analogues in marine bivalves and gastropods. The Panel on Contaminants in the Food Chain reviewed the available literature but did not find support for the minimum lethal dose for humans of 2 mg, mentioned in various reviews. Some human case reports describe serious effects at a dose of 0.2 mg, corresponding to 4 μg/kg body weight (bw). However, the uncertainties on the actual exposure in the studies preclude their use for derivation of an acute reference dose (ARfD). Instead, a group ARfD of 0.25 μg/kg bw, applying to TTX and its analogues, was derived based on a TTX dose of 25 μg/kg bw at which no apathy was observed in an acute oral study with mice, applying a standard uncertainty factor of 100. Estimated relative potencies for analogues are lower than that of TTX but are associated with a high degree of uncertainty. Based on the occurrence data submitted to EFSA and reported consumption days only, average and P95 exposures of 0.00–0.09 and 0.00–0.03 μg/kg bw, respectively, were calculated. Using a large portion size of 400 g bivalves and P95 occurrence levels of TTX, with exception of oysters, the exposure was below the group ARfD in all consumer groups. A concentration below 44 μg TTX equivalents/kg shellfish meat, based on a large portion size of 400 g, was considered not to result in adverse effects in humans. Liquid chromatography with tandem mass spectroscopy (LC–MS/MS) methods are the most suitable for identification and quantification of TTX and its analogues, with LOQs between 1 and 25 μg/kg.
Integrated modelling of urban spatial development under uncertain climate futures : A case study in Hungary
Li, Sen ; Juhász-Horváth, Linda ; Pedde, Simona ; Pintér, László ; Rounsevell, Mark D.A. ; Harrison, Paula A. - \ 2017
Environmental Modelling & Software 96 (2017). - ISSN 1364-8152 - p. 251 - 264.
Hungary - Integrated modelling - Integrated socioeconomic and climate change scenarios - Population distribution - Stakeholder - Urban land cover change

To provide fundamental decision support information for climate risk assessment in Hungary, an urban spatial development model of land cover change and population age structure dynamics was developed and applied to local integrated scenarios of climate change and stakeholder-derived socio-economic change. The four integrated scenarios for Hungary produced contrasting projections for urban patterns to 2100, but peri-urbanisation around Budapest was estimated to occur under all scenarios, together with a decline in working age population in the centres of the capital and major towns. This suggests that future urban planning needs to take into consideration the potential for underutilised urban infrastructure in the centre of the capital and pressures for social service provisioning in its outskirt. The integrated scenarios and model developed can be used in future studies to test the effectiveness of inter-sectoral policy responses in adapting urban planning to multiple climate and socio-economic challenges.

Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control
Horvath, Beatrix M. ; Kourova, Hana ; Nagy, Szilvia ; Nemeth, Edit ; Magyar, Zoltan ; Papdi, Csaba ; Ahmad, Zaki ; Sanchez-Perez, Gabino F. ; Perilli, Serena ; Blilou, Ikram ; Scheres, Ben - \ 2017
The EMBO Journal 36 (2017). - ISSN 0261-4189 - p. 1261 - 1278.
RETINOBLASTOMA RELATED - Arabidopsis - BRCA1 - DNA damage response - E2FA
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta. Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity.
Atmospheric measurements of Δ17O in CO2 in Göttingen, Germany reveal a seasonal cycle driven by biospheric uptake
Hofmann, M.E.G. ; Horváth, B. ; Schneider, L. ; Peters, W. ; Schützenmeister, K. ; Pack, A. - \ 2017
Geochimica et Cosmochimica Acta 199 (2017). - ISSN 0016-7037 - p. 143 - 163.
3D transport model - O - Carbon dioxide - Terrestrial gross primary production - TM5 - Triple oxygen isotopes - Troposphere - ΔO

The triple oxygen isotope composition of tropospheric CO2 might be a promising new tracer for terrestrial gross carbon fluxes. This notion is based on global box modeling of its abundance, and on highly challenging and therefore very sparse measurements of 16O, 17O and 18O in CO2 in the lower atmosphere. Here, we present additional high-precision triple oxygen isotope measurements of ambient air CO2 sampled in Göttingen (NW Germany) over the course of 2 years and of two air samples taken on top of the Brocken Mountain (1140 m, NW Germany). Göttingen differs from other locations where Δ17O was measured by its proximity to both urban sources of CO2, and to extensive uptake of CO2 by vegetation. In our analysis, we specifically try to discern this latter influence on our measurements, and to distinguish it from other known sources of variation in Δ17O. Our triple oxygen isotope data are reported as Δ17O values relative to a CO2-water equilibration line with Δ17O = ln (δ17O + 1) − 0.5229 × ln (δ18O + 1). We report an average of -0.02 ± 0.05‰ (SD) in the first year and -0.12 ± 0.04‰ (SD) in the second year of our measurements. This year-to-year difference is higher than expected based on other available Δ17O records, but careful scrutiny of our measurement approach did not reveal obvious analytical biases, leaving this aspect of our record unexplained. After removing the year-to-year trend, our time series shows a statistically robust seasonal cycle with maximum values in June/July and an amplitude (peak-to-trough) of 0.13 ± 0.02‰. We compare our observational data to a revised triple oxygen isotope mass balance “box” model of tropospheric CO2 where we reconcile both 18O/16O and 17O/16O fractionation processes. We also compare them to Göttingen-specific output from a three-dimensional transport model simulation of Δ17O in CO2 performed with the Tracer Model 5 (TM5). Both the modeled isofluxes at the surface, and the modeled stratospheric, fossil, and biospheric Δ17O components in the atmosphere at Göttingen confirm that the observed seasonal cycle in Δ17O is driven primarily by the seasonal cycle of gross primary productivity (GPP), and that the seasonal variations in both stratospheric transport and fossil fuel emissions play a minor role at our location. Our results therefore strengthen earlier suggestions that GPP is reflected in Δ17O, and call for more seasonally resolved measurements at continental locations like Göttingen.

GeneNetwork: framework for web-based genetics
Sloan, Zachary ; Arends, Danny ; Broman, Karl W. ; Centeno, Arthur ; Furlotte, Nicholas ; Nijveen, H. ; Yan, Lei ; Zhou, Xiang ; Williams, Robert W. ; Prins, Pjotr - \ 2016
The Journal of Open Source Software 1 (2016)2. - 3 p.
GeneNetwork (GN) is a free and open source (FOSS) framework for web-based genetics that can be deployed anywhere. GN allows biologists to upload high-throughput experimental data, such as expression data from microarrays and RNA-seq, and also `classic' phenotypes, such as disease phenotypes. These phenotypes can be mapped interactively against genotypes using embedded tools, such as R/QTL (Arends et al. 2010) mapping, interval mapping for model organisms and pylmm; an implementation of FaST-LMM (Lippert et al. 2011) which is more suitable for human populations and outbred crosses, such as the mouse diversity outcross. Interactive D3 graphics are included from R/qtlcharts and presentation-ready figures can be generated. Recently we have added functionality for phenotype correlation (Wang et al. 2016) and network analysis (Langfelder and Horvath 2008).
Expression data from Arabidopsis root tips rRBr mutant
Horvath, Beatrix M. ; Kourova, Hana ; Nagy, Szilvia ; Nemeth, Edit ; Magyar, Zoltan ; Papdi, Csaba ; Ahmad, Zaki ; Sanchez Perez, Gabino ; Perilli, Serena ; Blilou, Ikram ; Pettkó-Szandtner, Aladár ; Darula, Zsuzsanna ; Meszaros, Tamas ; Binarova, Pavla ; Bogre, Laszlo ; Scheres, Ben - \ 2015
Arabidopsis thaliana - GSE47715 - PRJNA207350
The RETINOBLASTOMA–RELATED (RBR) is a key regulator of cell proliferation and differentiation in plants, and plays an important role in maintenance of the stem cell niche in the root.
Plant responses to insect egg deposition
Hilker, M. ; Fatouros, N.E. - \ 2015
Annual Review of Entomology 60 (2015). - ISSN 0066-4170 - p. 493 - 515.
sogatella-furcifera horvath - elm leaf beetle - parasitoid anagrus-nilaparvatae - medfly ceratitis-capitata - oryza-sativa l. - defense responses - pieris-brassicae - host location - phytophagous insects - ovicidal substance
Plants can respond to insect egg deposition and thus resist attack by herbivorous insects from the beginning of the attack, egg deposition. We review ecological effects of plant responses to insect eggs and differentiate between egg-induced plant defenses that directly harm the eggs and indirect defenses that involve egg parasitoids. Furthermore, we discuss the ability of plants to take insect eggs as warning signals; the eggs indicate future larval feeding damage and trigger plant changes that either directly impair larval performance or attract enemies of the larvae. We address the questions of how egg-associated cues elicit plant defenses, how the information that eggs have been laid is transmitted within a plant, and which molecular and chemical plant responses are induced by egg deposition. Finally, we highlight evolutionary aspects of the interactions between plants and insect eggs and ask how the herbivorous insect copes with egg-induced plant defenses and may avoid them by counteradaptations.
Synergistic effects of direct and indirect defences on herbivore egg survival in a wild crucifer
Fatouros, N.E. ; Pineda, A. ; Huigens, M.E. ; Broekgaarden, C. ; Shimwela, M.M. ; Figueroa Candia, I.A. ; Verbaarschot, P. ; Bukovinszky, T. - \ 2014
Proceedings of the Royal Society. B: Biological Sciences 281 (2014)1789. - ISSN 0962-8452 - 9 p.
furcifera horvath homoptera - plant defense - trade-offs - antiherbivore defenses - natural enemies - fitness costs - brassica-rapa - resistance - oviposition - butterflies
Evolutionary theory of plant defences against herbivores predicts a trade-off between direct (anti-herbivore traits) and indirect defences (attraction of carnivores) when carnivore fitness is reduced. Such a trade-off is expected in plant species that kill herbivore eggs by exhibiting a hypersensitive response (HR)-like necrosis, which should then negatively affect carnivores. We used the black mustard (Brassica nigra) to investigate how this potentially lethal direct trait affects preferences and/or performances of specialist cabbage white butterflies (Pieris spp.), and their natural enemies, tiny egg parasitoid wasps (Trichogramma spp.). Both within and between black mustard populations, we observed variation in the expression of Pieris egg-induced HR. Butterfly eggs on plants with HR-like necrosis suffered lower hatching rates and higher parasitism than eggs that did not induce the trait. In addition, Trichogramma wasps were attracted to volatiles of egg-induced plants that also expressed HR, and this attraction depended on the Trichogramma strain used. Consequently, HR did not have a negative effect on egg parasitoid survival. We conclude that even within a system where plants deploy lethal direct defences, such defences may still act with indirect defences in a synergistic manner to reduce herbivore pressure.
Symbiont-mediated adaptation by planthoppers and leafhoppers to resistant rice varieties
Ferrater, J.B. ; Jong, P.W. de; Dicke, M. ; Chen, Y.H. ; Horgan, F.G. - \ 2013
Arthropod-Plant Interactions 7 (2013)6. - ISSN 1872-8855 - p. 591 - 605.
nilaparvata-lugens stal - yeast-like symbiote - sogatella-furcifera horvath - laodelphax-striatellus homoptera - nephotettix-cincticeps uhler - oryza-sativa l. - brown planthopper - whitebacked planthopper - histological observations - phylogenetic position
For over 50 years, host plant resistance has been the principal focus of public research to reduce planthopper and leafhopper damage to rice in Asia. Several resistance genes have been identified from native varieties and wild rice species, and some of these have been incorporated into high-yielding rice varieties through conventional breeding. However, adaptation by hoppers to resistant rice has been phenomenally rapid, and hopper populations with virulence against several resistance genes are now widespread. Directional genetic selection for virulent hoppers seems unlikely given the rapid pace of adaptation reported from field and laboratory studies. Among the alternative explanations for rapid hopper adaptation are changes (genetic, epigenetic, or community structure) in endosymbiont communities that become advantageous for planthoppers and leafhoppers that feed on resistant rice varieties. This review examines the nature of these symbiont communities and their functions in planthoppers and leafhoppers—focusing on their likely roles in mediating adaptation to plant resistance. Evidence from a small number of experimental studies suggests that bacterial and eukaryotic (including yeast-like) symbionts can determine or mediate hopper virulence on rice plants and that symbiont functions could change over successive generations of selection on both resistant and susceptible plants. The review highlights the potential complexity of rice hopper–symbiont interactions and calls for a more careful choice of research materials and methods to help reduce this complexity. Finally, the consequences of symbiont-mediated virulence adaptation for future rice breeding programs are discussed.
Naturally occurring allele diversity allows potato cultivation in northern latitudes
Kloosterman, B.A. ; Abelenda, J.A. ; Carretero Gomez, M. ; Oortwijn, M.E.P. ; Boer, J.M. de; Kowitwanich, K. ; Horvath, B.M. ; Eck, H.J. van; Smaczniak, C. ; Prat, S. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
Nature 495 (2013)7440. - ISSN 0028-0836 - p. 246 - 250.
flowering-time - arabidopsis - constans - tuberization - gene - plants - fkf1
Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors1 and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal2. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and isone of the world’s most important food crops. This annual plant originates from the Andean regions of South America3. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type4 is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.
Insect egg deposition induces indirect defense and epicuticular wax changes in Arabidopsis thaliana
Blenn, B. ; Bandoly, M. ; Küffner, A. ; Otte, T. ; Geiselhardt, S. ; Fatouros, N.E. ; Hilker, M. - \ 2012
Journal of Chemical Ecology 38 (2012)7. - ISSN 0098-0331 - p. 882 - 892.
furcifera horvath homoptera - plant cuticular waxes - whitebacked planthopper - eceriferum mutants - trissolcus-basalis - pierid butterflies - nezara-viridula - host location - up-regulation - rice plants
Egg deposition by the Large Cabbage White butterfly Pieris brassicae on Brussels sprouts plants induces indirect defense by changing the leaf surface, which arrests the egg parasitoid Trichogramma brassicae. Previous studies revealed that this indirect defense response is elicited by benzyl cyanide (BC), which is present in the female accessory reproductive gland (ARG) secretion and is released to the leaf during egg deposition. Here, we aimed (1) to elucidate whether P. brassicae eggs induce parasitoid-arresting leaf surface changes in another Brassicacean plant, i.e., Arabidopsis thaliana, and, if so, (2) to chemically characterize the egg-induced leaf surface changes. Egg deposition by P. brassicae on A. thaliana leaves had similar effects to egg deposition on Brussels sprouts with respect to the following: (a) Egg deposition induced leaf surface changes that arrested T. brassicae egg parasitoids. (b) Application of ARG secretion of mated female butterflies or of BC to leaves had the same inductive effects as egg deposition. Based on these results, we conducted GC-MS analysis of leaf surface compounds from egg- or ARG-induced A. thaliana leaves. We found significant quantitative differences in epicuticular waxes compared to control leaves. A discriminant analysis separated surface extracts of egg-laden, ARG-treated, untreated control and Ringer solution-treated control leaves according to their quantitative chemical composition. Quantities of the fatty acid tetratriacontanoic acid (C34) were significantly higher in extracts of leaf surfaces arresting the parasitoids (egg-laden or ARG-treated) than in respective controls. In contrast, the level of tetracosanoic acid (C24) was lower in extracts of egg-laden leaves compared to controls. Our study shows that insect egg deposition on a plant can significantly affect the quantitative leaf epicuticular wax composition. The ecological relevance of this finding is discussed with respect to its impact on the behavior of egg parasitoids.
Plant Volatiles Induced by Herbivore Egg Deposition Affect Insects of Different Trophic Levels
Fatouros, N.E. ; Lucas-Barbosa, D. ; Weldegergis, B.T. ; Pashalidou, F.G. ; Loon, J.J.A. van; Dicke, M. ; Harvey, J.A. ; Gols, R. ; Huigens, M.E. - \ 2012
PLoS One 7 (2012)8. - ISSN 1932-6203
furcifera horvath homoptera - elm leaf beetle - whitebacked planthopper - cotesia-glomerata - herbaceous plants - pieris-brassicae - host location - rice plants - oviposition - defense
Plants release volatiles induced by herbivore feeding that may affect the diversity and composition of plant-associated arthropod communities. However, the specificity and role of plant volatiles induced during the early phase of attack, i.e. egg deposition by herbivorous insects, and their consequences on insects of different trophic levels remain poorly explored. In olfactometer and wind tunnel set-ups, we investigated behavioural responses of a specialist cabbage butterfly (Pieris brassicae) and two of its parasitic wasps (Trichogramma brassicae and Cotesia glomerata) to volatiles of a wild crucifer (Brassica nigra) induced by oviposition of the specialist butterfly and an additional generalist moth (Mamestra brassicae). Gravid butterflies were repelled by volatiles from plants induced by cabbage white butterfly eggs, probably as a means of avoiding competition, whereas both parasitic wasp species were attracted. In contrast, volatiles from plants induced by eggs of the generalist moth did neither repel nor attract any of the tested community members. Analysis of the plant’s volatile metabolomic profile by gas chromatography-mass spectrometry and the structure of the plant-egg interface by scanning electron microscopy confirmed that the plant responds differently to egg deposition by the two lepidopteran species. Our findings imply that prior to actual feeding damage, egg deposition can induce specific plant responses that significantly influence various members of higher trophic levels.
Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes
Magyar, Z. ; Horvath, B. ; Khan, S. ; Scheres, B. - \ 2012
The EMBO Journal 31 (2012). - ISSN 0261-4189 - p. 1480 - 1493.
retinoblastoma-related protein - cyclin-dependent kinase - genome-wide identification - stem-cell maintenance - a-type cyclin - transcription factor - leaf development - dna-replication - plant development - follicle cells
Post-embryonic growth in plants depends on the continuous supply of undifferentiated cells within meristems. Proliferating cells maintain their competence for division by active repression of differentiation and the associated endocycle entry. We show by upregulation and downregulation of E2FA that it is required for maintaining proliferation, as well as for endocycle entry. While E2FB–RBR1 (retinoblastoma-related protein 1) complexes are reduced after sucrose addition or at elevated CYCD3;1 levels, E2FA maintains a stable complex with RBR1 in proliferating cells. Chromatin immunoprecipitation shows that RBR1 binds in the proximity of E2F promoter elements in CCS52A1 and CSS52A2 genes, central regulators for the switch from proliferation to endocycles. Overexpression of a truncated E2FA mutant (E2FA¿RB) lacking the RBR1-binding domain interferes with RBR1 recruitment to promoters through E2FA, leading to decreased meristem size in roots, premature cell expansion and hyperactivated endocycle in leaves. E2F target genes, including CCS52A1 and CCS52A2, are upregulated in E2FA¿RB and e2fa knockout lines. These data suggest that E2FA in complex with RBR1 forms a repressor complex in proliferating cells to inhibit premature differentiation and endocycle entry. Thus, E2FA regulates organ growth via two distinct, sequentially operating pathways.
Why Peter should not retire - an empirical analysis of the co-evolution of Peter’s publications and citations
Horvath, Cs ; Kornelis, M. - \ 2011
In: Liber Amicorum in honor of Peter S.H. Leeflang, Groningen / Wieringa, J.E., Verhoef, P.C., Hoekstra, J.C., Groningen : Rijksuniversiteit Groningen - ISBN 9789036750493 - p. 17 - 27.
Atmospheric composition change: Ecosystems-Atmosphere interactions
Fowler, D. ; Pilegaard, K. ; Sutton, M.A. ; Ambus, P. ; Raivonen, M. ; Duyzer, J. ; Simpson, D. ; Fagerli, H. ; Fuzzi, S. ; Schjoerring, J.K. ; Granier, C. ; Neftel, A. ; Isaksen, I.S.A. ; Laj, P. ; Maione, M. ; Monks, P.S. ; Burkhardt, J. ; Daemmgen, U. ; Neirynck, J. ; Personne, E. ; Wichink Kruit, R.J. ; Butterbach-Bahl, K. ; Flechard, C. ; Tuovinen, J.P. ; Coyle, M. ; Gerosa, G. ; Loubet, B. ; Altimir, N. ; Gruenhage, L. ; Ammann, C. ; Cieslik, S. ; Paoletti, E. ; Mikkelsen, T.N. ; Ro-Poulsen, H. ; Cellier, P. ; Cape, J.N. ; Horvath, L. ; Loreto, F. ; Niinemets, U. ; Palmer, P.I. ; Rinne, J. ; Misztal, P. ; Nemitz, E. ; Nilsson, D. ; Pryor, S. ; Gallagher, M.W. ; Vesala, T. ; Skiba, U. ; Brueggemann, N. ; Zechmeister-Boltenstern, S. ; Williams, J. ; O'Dowd, C. ; Facchini, M.C. ; Leeuw, G. de; Flossman, A. ; Chaumerliac, N. ; Erisman, J.W. - \ 2009
Atmospheric Environment 43 (2009)33. - ISSN 1352-2310 - p. 5193 - 5267.
volatile organic-compounds - relaxed eddy accumulation - dry deposition velocity - reaction mass-spectrometry - cloud condensation nuclei - gas-particle interactions - surface-exchange fluxes - nitric-oxide emissions - beech fagus-sylvatica - ozone risk-assessment
Ecosystems and the atmosphere: This review describes the state of understanding the processes involved in the exchange of trace gases and aerosols between the earth's surface and the atmosphere. The gases covered include NO, NO2, HONO, HNO3, NH3, SO2, DMS, Biogenic VOC, O-3, CH4, N2O and particles in the size range 1 nm-10 mu m including organic and inorganic chemical species. The main focus of the review is on the exchange between terrestrial ecosystems, both managed and natural and the atmosphere, although some new developments in ocean-atmosphere exchange are included. The material presented is biased towards the last decade, but includes earlier work, where more recent developments are limited or absent. New methodologies and instrumentation have enabled, if not driven technical advances in measurement. These developments have advanced the process understanding and upscaling of fluxes, especially for particles, VOC and NH3. Examples of these applications include mass spectrometric methods, such as Aerosol Mass Spectrometry (AMS) adapted for field measurement of atmosphere-surface fluxes using micrometeorological methods for chemically resolved aerosols. Also briefly described are some advances in theory and techniques in micrometeorology. For some of the compounds there have been paradigm shifts in approach and application of both techniques and assessment. These include flux measurements over marine surfaces and urban areas using micrometeorological methods and the up-scaling of flux measurements using aircraft and satellite remote sensing. The application of a flux-based approach in assessment of O-3 effects on vegetation at regional scales is an important policy linked development secured through improved quantification of fluxes. The coupling of monitoring, modelling and intensive flux measurement at a continental scale within the NitroEurope network represents a quantum development in the application of research teams to address the underpinning science of reactive nitrogen in the cycling between ecosystems and the atmosphere in Europe. Some important developments of the science have been applied to assist in addressing policy questions, which have been the main driver of the research agenda, while other developments in understanding have not been applied to their wider field especially in chemistry-transport models through deficiencies in obtaining appropriate data to enable application or inertia within the modelling community. The paper identifies applications, gaps and research questions that have remained intractable at least since 2000 within the specialized sections of the paper, and where possible these have been focussed on research questions for the coming decade. (C) 2009 Published by Elsevier Ltd.
Soil-plant interrelations: the significance of soil degradation and the risk assessment methodology for salinization
Hagyó, A. ; Tóth, T. ; Bloem, E. ; Zee, S.E.A.T.M. van der; Horváth, E. - \ 2008
In: 7th Alps-Adria Scientific Workshop, 27 April 1st May, 2008, Stara Lesna, Slovakia. - S : - p. 1579 - 1582.
Numerous methodologies are used in the EU Member States to assess the risk for different soil threats related to various agricultural practices (erosion, salinisation, organic matter decline, compaction and landslides). Our aim was to evaluate the risk assessment methodologies (RAMs) utilized for salinization in the Member States based on questionnaires sent to experts and policy makers. A first analysis of the obtained information reveals that most countries affected by the problem do not have official methodology and some countries do not have any methodology at all. Hungary has an officially recognized assessment. Slovakia and Spain has a RAM used by scientists. Greece and Cyprus provided information about RAM that they would prefer. Salt-affected soils occur in Bulgaria, France, Italy and Romania also, but we didn't get answer from these countries. To fill the information gaps we need a further analysis on scientific papers
Full accounting of the greenhouse gas (CO2, N2O, CH4) budget of nine European grassland sites
Soussana, J.F. ; Allard, V. ; Pilegaard, K. ; Ambus, P. ; Amman, C. ; Campbell, C. ; Ceschia, E. ; Clifton-Brown, J. ; Czobel, S. ; Domingues, R. ; Flechard, C. ; Fuhrer, J. ; Hensen, A. ; Horvath, L. ; Jones, M. ; Kasper, G.J. ; Martin, C. ; Nagy, Z. ; Neftel, A. ; Raschi, A. ; Baronti, S. - \ 2007
Agriculture, Ecosystems and Environment 121 (2007)39479. - ISSN 0167-8809 - p. 121 - 134.
native tallgrass prairie - nitrous-oxide emissions - net ecosystem exchange - soil carbon - agricultural soils - primary productivity - land management - respiration - sequestration - dioxide
The full greenhouse gas balance of nine contrasted grassland sites covering a major climatic gradient over Europe was measured during two complete years. The sites include a wide range of management regimes (rotational grazing, continuous grazing and mowing), the three main types of managed grasslands across Europe (sown, intensive permanent and semi-natural grassland) and contrasted nitrogen fertilizer supplies. At all sites, the net ecosystem exchange (NEE) of CO2 was assessed using the eddy covariance technique. N2O emissions were monitored using various techniques (GC-cuvette systems, automated chambers and tunable diode laser) and CH4 emissions resulting from enteric fermentation of the grazing cattle were measured in situ at four sites using the SF6 tracer method. Averaged over the two measurement years, net ecosystem exchange (NEE) results show that the nine grassland plots displayed a net sink for atmospheric CO2 of -240 +/- 70 g C m(-2) year(-1) (mean confidence interval at p > 0.95). Because of organic C exports (from cut and removed herbage) being usually greater than C imports (from manure spreading), the average C storage (net biome productivity, NBP) in the grassland plots was estimated at -104 +/- 73 g cm(-2) year(-1) that is 43% of the atmospheric CO2 sink. On average of the 2 years, the grassland plots displayed annual N2O and CH4 (from enteric fermentation by grazing cattle) emissions, in CO2-C equivalents, of 14 +/- 4.7 and 32 +/- 6.8 g CO2-C equiv. m(-2) year(-1), respectively. Hence, when expressed in CO2-C equivalents, emissions of N2O and CH4 resulted in a 19% offset of the NEE sink activity. An attributed GHG balance has been calculated by subtracting from the NBP: (i) N2O and CH4 emissions occurring within the grassland plot and (ii) off-site emissions of CO2 and CH4 as a result of the digestion and enteric fermentation by cattle of the cut herbage. On average of the nine sites, the attributed GHG balance was not significantly different from zero (-85 +/- 77 g CO2-C equiv. m(-2) year(-1)).
Challenges in quantifying biosphere-atmosphere exchange of nitrogen species.
Sutton, M.A. ; Nemitz, E. ; Erisman, J.W. ; Beier, C. ; Butterbach-Bahl, K. ; Cellier, P. ; Vries, W. de; Cotrufo, F. ; Skiba, U. ; Marco, C. Di; Jones, S. ; Laville, P. ; Soussana, J.F. ; Loubet, B. ; Twigg, M. ; Famulari, D. ; Whitehead, J. ; Gallagher, M.W. ; Neftel, A. ; Flechard, C.R. ; Herrmann, B. ; Calanca, P.L. ; Schjoerring, J.K. ; Daemmgen, U. ; Horvath, L. ; Tang, Y.S. ; Emmet, B.A. ; Tietema, A. ; Penuelas, J. ; Kesik, M. ; Brueggemann, N. ; Pilegaard, K. ; Vesala, T. ; Campbell, C.L. ; Olesen, J.E. ; Dragosits, U. ; Theobald, M.R. ; Levy, P. ; Mobbs, D.C. ; Milne, R. ; Viovy, N. ; Vuichard, N. ; Smith, J.U. ; Smith, P. ; Bergamaschi, P. ; Fowler, D. ; Reis, S. Dos - \ 2007
Environmental Pollution 150 (2007)1. - ISSN 0269-7491 - p. 125 - 139.
gas-particle interactions - surface-exchange - simulation-model - ammonia exchange - dutch heathland - climate-change - oxide fluxes - trace gases - deposition - soil
Recent research in nitrogen exchange with the atmosphere has separated research communities according to N form. The integrated perspective needed to quantify the net effect of N on greenhouse-gas balance is being addressed by the NitroEurope Integrated Project (NEU). Recent advances have depended on improved methodologies, while ongoing challenges include gas¿aerosol interactions, organic nitrogen and N2 fluxes. The NEU strategy applies a 3-tier Flux Network together with a Manipulation Network of global-change experiments, linked by common protocols to facilitate model application. Substantial progress has been made in modelling N fluxes, especially for N2O, NO and bi-directional NH3 exchange. Landscape analysis represents an emerging challenge to address the spatial interactions between farms, fields, ecosystems, catchments and air dispersion/deposition. European up-scaling of N fluxes is highly uncertain and a key priority is for better data on agricultural practices. Finally, attention is needed to develop N flux verification procedures to assess compliance with international protocols.
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