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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Assessing the influences of ecological restoration on perceptions of cultural ecosystem services by residents of agricultural landscapes of western China
Dou, Yuehan ; Zhen, Lin ; Yu, Xiubo ; Bakker, Martha ; Carsjens, Gerrit Jan ; Xue, Zhichao - \ 2019
Science of the Total Environment 646 (2019). - ISSN 0048-9697 - p. 685 - 695.
Agricultural landscapes - Cultural ecosystem services - Ecological restoration - Household survey - Human perception

Landscape change caused by ecological restoration projects has both positive and negative influences on human livelihoods, yet surprisingly little research on the cultural consequences of ecological restoration in agricultural landscapes has taken place. Cultural consequences can be captured in the ecosystem services framework as cultural ecosystem services (CES). However, assessment and valuation of these services to support decision-making for this essential ecosystem is lacking. To help fill this gap, we assessed the opinions of Chinese rural communities about CES and the changes in their perception under the Grain for Green program (GFG), a nationwide program to relieve the pressure on ecosystems (soil erosion and land degradation) by converting cultivated land or barren land on steep slopes into grassland and forests. We used Guyuan City in China's Ningxia Hui Autonomous Region as a case study, using a workshop to identify the CES provided by the agricultural landscape, followed by semi-structured household interviews to quantify perceptions of these CES. We found that all eight CES types identified by the workshop were perceived by the rural communities. Reforestation changed their perceptions of CES directly due to land cover change and indirectly due to the resulting economic changes and migration of mostly young workers in search of better jobs. Cultivated land was perceived as more important than forest for CES provision. In addition, residential areas were perceived as providing significant CES because of local traditions that produce close and highly social neighborhood bonds in agricultural landscapes.

WUR bloembollen verhuist naar Bleiswijk
Bakker, Sjaak ; Poot, Eric - \ 2018
Ditr P79_Characterisation of PLETHORA during gall formation of the root-knot nematode Meloidogyne incognita
Oosterbeek, Matthijs ; Overmars, H.A. ; Scheres, B.J.G. ; Bakker, J. ; Goverse, A. - \ 2018
The parasitic root-knot nematode Meloidogyne incognita manipulates developmental processes in plants through formation of large tumour-like structures, designated as galls, in the roots of their hosts. The transcriptional profile of these galls show significant overlap with that of the formation of lateral roots (Cabrera et al., 2014). Key regulators in the formation of lateral roots are the PLETHORA (PLT) transcription factors PLT3, PLT5 and PLT7. They are induced by the sustained presence of the phytohormone auxin. These genes work together to regulate positioning and outgrowth of lateral root primordia (Hofhuis et al., 2013). The auxin efflux proteins PINFORMED (PIN) are thought to play an important role in this process and PLTs are known to regulate them in plants (Prasad et al., 2011). During the initial development of nematode-induced galls an accumulation of auxin is observed (Karczmarek et al., 2004). Additionally PIN proteins are known to be involved in gall formation (Kyndt et al., 2016). However, how the PIN proteins are regulated upon root-knot nematode infection is unknown. Hence, we studied the possibility that the PLT-PIN module is used during the formation of feeding sites of M. incognita. Mutant lines of the PLT genes showed a decrease in the number of infections and in number of reproducing females as compared to the wild type lines. Additionally, in several mutant lines galls developed that were significantly increased in size. Moreover, the auxin exporter PIN3 in the mutant line of the three PLT genes was no longer localised at the plasma membranes of cells within the feeding site in contrast to the wild type lines. We conclude that the three PLT genes are involved in feeding site initiation and development and could potentially achieve this through regulation of PIN.
Can the Land Use Master Plan Control Urban Expansion and Protect Farmland in China? A Case Study of Nanjing
Shao, Zinan ; Spit, Tejo ; Jin, Zhifeng ; Bakker, Martha ; Wu, Qun - \ 2018
Growth and Change 49 (2018)3. - ISSN 0017-4815 - p. 512 - 531.

Urbanization represents a challenge for plans aimed at controlling urban expansion and protecting farmland, such as the land use master plan (LUMP) instituted by the Chinese national government. This paper studies the effectiveness of such top–down plans under the authoritarian regime through the case study of Nanjing. In contrast to previous studies that compare actual and planned land-use maps, we compare actual and planned land-use patterns. We use land-use change data to examine spatio-temporal land-use change between the years 1997 and 2014. The results indicate that the actual amount of urban-rural built-up land exceeded planned regulatory amount by 50,185 ha and the total farmland was 70,541 ha less than the target outlined in the LUMP (1997–2010). Based on these results, and the fact that the allowed total urban-rural built-up land had already been surpassed in 2014, it is to be expected that the target of farmland protection outlined in the LUMP (2006–2020) will be broken, signaling the ineffectiveness of the plan to control urban expansion and protect farmland. Plan-led developments (e.g., new towns, development zones) and market forces (e.g., housing market, foreign direct investment) explain these developments. This study indicates that when cities embrace “growth-led” development and entrepreneurial governance, the ability of plans to control urban expansion and protect farmland is severely limited.

Changes in root architecture of Arabidopsis thaliana induced by the cyst nematode Heterodera schachtii
Willig, J. ; Sonneveld, Devon ; Sterken, M.G. ; Lozano Torres, J.L. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Low levels of infection by cyst nematodes on some resistant crop varieties result in significant loss in yield, while other heavily infected varieties show hardly any symptoms at all. This difference in responses suggests that some plants tolerate biotic stress by plant parasitic nematodes better than others. The objective of our current research is to investigate whether Arabidopsis thaliana can be used to unravel the genetic architecture and molecular mechanisms underlying differences in tolerance to plant parasitic nematodes in plants. To this end we first looked at changes in root architecture upon inoculation with increasing numbers of the beet cyst nematode Heterodera schachtii. This revealed how plants could compensate for damage induced by cyst nematodes in roots at low inoculation densities. Altogether, our data may demonstrate if Arabidopsis can be used as a model to study tolerance to cyst nematodes in plants.
Minder watergebruik in tuinbouw Saudi-Arabië
Bakker, J.C. - \ 2018
Onder Glas 15 (2018)5. - p. 43 - 43.
Warming enhances sedimentation and decomposition of organic carbon in shallow macrophyte-dominated systems with zero net effect on carbon burial
Velthuis, Mandy ; Kosten, Sarian ; Aben, Ralf ; Kazanjian, Garabet ; Hilt, Sabine ; Peeters, Edwin T.H.M. ; Donk, Ellen van; Bakker, Elisabeth S. - \ 2018
Global Change Biology (2018). - ISSN 1354-1013
carbon cycle - decomposition - global warming - mineralization - phenology - primary production - sedimentation - submerged aquatic plant

Temperatures have been rising throughout recent decades and are predicted to rise further in the coming century. Global warming affects carbon cycling in freshwater ecosystems, which both emit and bury substantial amounts of carbon on a global scale. Currently, most studies focus on the effect of warming on overall carbon emissions from freshwater ecosystems, while net effects on carbon budgets may strongly depend on burial in sediments. Here, we tested whether year-round warming increases the production, sedimentation, or decomposition of particulate organic carbon and eventually alters the carbon burial in a typical shallow freshwater system. We performed an indoor experiment in eight mesocosms dominated by the common submerged aquatic plant Myriophyllum spicatum testing two temperature treatments: a temperate seasonal temperature control and a warmed (+4°C) treatment (n = 4). During a full experimental year, the carbon stock in plant biomass, dissolved organic carbon in the water column, sedimented organic matter, and decomposition of plant detritus were measured. Our results showed that year-round warming nearly doubled the final carbon stock in plant biomass from 6.9 ± 1.1 g C in the control treatment to 12.8 ± 0.6 g C (mean ± SE), mainly due to a prolonged growing season in autumn. DOC concentrations did not differ between the treatments, but organic carbon sedimentation increased by 60% from 96 ± 9.6 to 152 ± 16 g C m−2 yaer−1 (mean ± SE) from control to warm treatments. Enhanced decomposition of plant detritus in the warm treatment, however, compensated for the increased sedimentation. As a result, net carbon burial was 40 ± 5.7 g C m−2 year−1 in both temperature treatments when fluxes were combined into a carbon budget model. These results indicate that warming can increase the turnover of organic carbon in shallow macrophyte-dominated systems, while not necessarily affecting net carbon burial on a system scale.

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation
Remmers, Ilse M. ; Adamo, Sarah D'; Martens, Dirk E. ; Vos, Ric C.H. de; Mumm, Roland ; America, Antoine H.P. ; Cordewener, Jan H.G. ; Bakker, Linda V. ; Peters, Sander A. ; Wijffels, René H. ; Lamers, Packo P. - \ 2018
Algal Research 35 (2018). - ISSN 2211-9264 - p. 33 - 49.
Diatoms - Diurnal metabolism - Lipids - Mitochondrion - Omics - Triacylglycerol

Nitrogen deprivation increases the triacylglycerol (TAG) content in microalgae but also severely decreases the growth rate. Most approaches that attempted to increase TAG productivity by overexpression or knockdown of specific genes related to the regulation of the lipid synthesis have reported only little success. More insight into the molecular mechanisms related to lipid accumulation and impaired growth rate is needed to find targets for improving TAG productivity. By using the emerging “omics” approach, we comprehensively profiled the physiology, transcriptome, proteome and metabolome of the diatom Phaeodactylum tricornutum during steady state growth at both nitrogen limited and replete levels during light:dark cycles. Under nitrogen limited conditions, 22% (2699) of the total identified transcripts, 17% (543) of the proteins and 44% (345) of the metabolites were significantly differentially regulated compared to nitrogen replete growth conditions. Although nitrogen limitation was responsible for the majority of significant differential transcript, protein and metabolite accumulation, we also observed differential expression over a diurnal cycle. Nitrogen limitation mainly induced an upregulation of nitrogen fixation, central carbon metabolism and TCA cycle, while photosynthetic and ribosomal protein synthesis are mainly downregulated. Regulation of the lipid metabolism and the expression of predicted proteins involved in lipid processes suggest that lipid rearrangements may substantially contribute to TAG distribution. However, TAG synthesis is also limited by the reduced carbon flux through central metabolism. Future strain improvements should therefore focus on understanding and improving the carbon flux through central carbon metabolism, selectivity and activity of DGAT isoforms and lipase enzymes.

An Evaluation of the Loss-on-Ignition Method for Determining the Soil Organic Matter Content of Calcareous Soils
Hoogsteen, M.J.J. ; Lantinga, E.A. ; Bakker, E.J. ; Tittonell, P.A. - \ 2018
Communications in Soil Science and Plant Analysis 48 (2018)13. - ISSN 0010-3624 - p. 1541 - 1552.
Calcite analysis procedures - ignition temperature - sample weight

The Loss-on-Ignition (LOI) method is widely employed for measuring the organic matter (OM) content of soil samples. There is a risk of carbonate losses when calcareous soil samples are analyzed through LOI, but this has never been investigated in detail. Moreover, a worldwide standard protocol for determining the carbonate content of soils is not available. The aims of this study were (i) to evaluate two commonly employed carbonate analysis procedures using calcareous and non-calcareous soil samples: the gravimetric method with (GMF) and without (GM) the addition of the antioxidant iron(II) chloride (FeCl2) and the acetic acid dissolution procedure (AAD); (ii) to evaluate the effect of ignition temperature on losses of pure calcite, calcite-quartz and calcareous soil samples. We found that the average apparent carbonate content of the non-calcareous soils was greatest for the GMF method followed by the AAD procedure. The GM method showed the smallest apparent carbonate contents. For the calcite-quartz sand mixture, ignition losses started at 600°C and increased with temperature in a sigmoidal way. LOI values stabilized at 750°C when 80% of the carbon dioxide was released. We recommend the GM procedure for carbonate analysis because the apparent carbonate contents of the non-calcareous soil samples were smallest. Furthermore, we recommend an LOI temperature of 550°C because at this ignition temperature 99.8% of the total calcite fraction remains in the soil samples.

Dietary Approach to Stop Hypertension (DASH) diet and risk of renal function decline and all-cause mortality in renal transplant recipients
Osté, Maryse C.J. ; Gomes-Neto, António W. ; Corpeleijn, Eva ; Gans, Rijk O.B. ; Borst, Martin H. de; Berg, Else van den; Soedamah-Muthu, Sabita S. ; Kromhout, Daan ; Navis, Gerjan J. ; Bakker, Stephan J.L. - \ 2018
American Journal of Transplantation (2018). - ISSN 1600-6135
Clinical research/practice - Graft survival - Kidney transplantation/nephrology - Nutrition - Patient survival
Renal transplant recipients (RTR) are at risk of decline of graft function and premature mortality, with high blood pressure as an important risk factor for both. To study the association of the Dietary Approach to Stop Hypertension (DASH) diet with these adverse events, we conducted a prospective cohort study of adult RTR. Dietary data were collected using a validated 177-item food frequency questionnaire and an overall DASH-score was obtained. We included 632 stable RTR (mean ± standard deviation age 53.0 ± 12.7 years, 57% men). Mean DASH score was 23.8 ± 4.7. During median follow-up of 5.3 (interquartile range, 4.1-6.0) years, 119 (18.8%) RTR had renal function decline, defined as a combined endpoint of doubling of serum creatinine and death-censored graft failure, and 128 (20.3%) died. In Cox-regression analyses, RTR in the highest tertile of the DASH score had lower risk of both renal function decline (hazard ratio [HR] = 0.57; 95% confidence interval [CI], 0.33-0.96, P = .03) and all-cause mortality (HR = 0.52; 95%CI, 0.32-0.83, P = .006) compared to the lowest tertile, independent of potential confounders. Adherence to a DASH-style diet is associated with lower risk of both renal function decline and all-cause mortality. These results suggest that a healthful diet might benefit long-term outcome in RTR.
Changes in shoot and root architecture of Arabidopsis thaliana by increasing inoculum densities of the cyst nematode Heterodera schachtii
Willig, J. ; Sonneveld, Devon ; Sterken, M.G. ; Lozano Torres, J.L. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Some crop varieties show significant loss in biomass even though these are resistant to cyst nematodes. Interestingly, some non-resistant varieties show no symptoms at all. This phenotypical variation is also known as tolerance. In agronomic context, tolerant crop varieties are able to withstand injury and produce acceptable yields. Because of environmental and practical reasons, it is difficult to eradicate below-ground pathogens. Despite the increasing need for tolerance to below-ground pathogens, breeding for tolerance is not yet applied. This has 4 reasons:
1. Disease tolerance for soil-pathogens is difficult to quantify.
2. Unknown if there is enough useful quantitative variation in disease tolerance to soil-pathogens in different ecotypes.
3. The genetic complexity of disease tolerance is not well understood.
4. It is unclear whether disease tolerance has a negative effect on desirable traits.
This research focusses on investigating whether Arabidopsis thaliana could be used as a model plant to detect polymorphic alleles and the recombination or segregation of these alleles that are coding for tolerance.
Exploring the Resistosome of the Potato CC-NB-LRR Immune Receptor Rx1
Sukarta, O.C.A. ; Slootweg, E.J. ; Boeren, J.A. ; Roosien, J. ; Pomp, H. ; Bakker, J. ; Smant, G. ; Goverse, A. - \ 2018
The potato Rx1 is an intracellular Nucleotide-binding Leucine Rich Repeat (NLR) immune receptor with an archetypical N-terminal coiled-coil (CC) domain. It confers extreme resistance against Potato Virus X (PVX) by gene-specific recognition of the viral coat protein (CP). Recent findings point to a role of Rx1 in the nucleus whereby it could directly bind host genetic material, though it remains unclear how this process eventually leads to defence. A possibility is that Rx1 recruits other host factors, for example via the CC domain, which is predicted to act as scaffolds for nuclear signalling. Here, we used the CC domains of Rx1 and the Rx1-like protein Gpa2 (mediates defence against the nematode Globodera pallida) as baits in a Co-IP/MS analysis after cell fractionation to co-purify putative interactors from Nicotiana benthamiana. Five hits (designated Rp01-Rp05) were further prioritized as candidate Rx1/Gpa2 interacting proteins. Similar pull-down experiments confirmed complex formation with the full-length immune receptors in plantae. Interestingly, co-expression of Rp05 alters the subcellular distribution of the Rx1-CC domain, hinting its role in Rx1-function. Transient overexpression experiments confirm that Rp05 could in fact potentiate defense against PVX. Interestingly, however, this occurs independently of Rx1. We substantiated this model by demonstrating that Rp05 could influence HR-responses by other NLR proteins (e.g. Gpa2, Sw5A/B and Mi-1) indicating that it may be a common downstream component in immune signaling. Currently, we focus on elucidating the detailed molecular underpinning of Rp05 function in R-gene mediated resistances using Rx1 as the principal model system.
Hydrofysische gegevens van de bodem in BRO en BIS : Update 2017
Bakker, G. ; Heinen, M. ; Groot, W.J.M. de; Assinck, F.B.T. ; Gooren, H.P.A. ; Hummelink, E.W.J. - \ 2018
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2895) - 95
Hydrofysische gegevens van de bodem, ofwel bodemgegevens die een sterke relatie hebben met het gedrag van water in de bodem, zijn belangrijke basisgegevens bij het modelleren van transport van water en opgeloste stoffen in de onverzadigde zone, maar zijn ook belangrijk in tal van andere toepassingen. Voorbeelden van hydrofysische bodemgegevens zijn met name de waterretentie- en doorlatendheidskarakteristiek, maar ook het organische stofgehalte, textuurgegevens, profielbeschrijving en andere metagegevens. Omdat er grote behoefte is aan actuele gegevens van hoge kwaliteit en omdat de huidige databases nog onvoldoende opschalingsmogelijkheden bieden, worden in dit project aanvullende kwalitatief hoogwaardige gegevens gegenereerd. De hydrofysische gegevens van de bodem en de bijbehorende beschrijvende gegevens zijn ondergebracht in het BIS (Bodem Informatie Systeem) en worden in de nabije toekomst ook ondergebracht in de BRO.
Momenteel zijn er 181 monsters, gekoppeld aan profielbeschrijvingen en andere meta-informatie, in BIS opgenomen.
Complexity in land use change; the case of the Dutch dairy sector
Groeneveld, Anouschka - \ 2018
University. Promotor(en): Wim Heijman, co-promotor(en): Jack Peerlings; Martha Bakker. - Wageningen : Wageningen University - ISBN 9789463437646 - 205
Quantification of chemical and mechanical bioerosion rates of six Caribbean excavating sponge species found on the coral reefs of Curaçao
Bakker, Didier M. de; Webb, Alice E. ; Bogaart, Lisanne A. van den; Heuven, Steven M.A.C. van; Meesters, Erik H. ; Duyl, Fleur C. van - \ 2018
PLoS One 13 (2018)5. - ISSN 1932-6203

Excavating sponges are among the most important macro-eroders of carbonate substrates in marine systems. Their capacity to remove substantial amounts of limestone makes these animals significant players that can unbalance the reef carbonate budget of tropical coral reefs. Nevertheless, excavating sponges are currently rarely incorporated in standardized surveys and experimental work is often restricted to a few species. Here were provide chemical and mechanical bioerosion rates for the six excavating sponge species most commonly found on the shallow reef of Curaçao (southern Caribbean): Cliona caribbaea, C. aprica, C. delitrix, C. amplicavata, Siphonodictyon brevitubulatum and Suberea flavolivescens. Chemical, mechanical and total bioerosion rates were estimated based on various experimental approaches applied to sponge infested limestone cores. Conventional standing incubation techniques were shown to strongly influence the chemical dissolution signal. Final rates, based on the change in alkalinity of the incubation water, declined significantly as a function of incubation time. This effect was mitigated by the use of a flow-through incubation system. Additionally, we found that mechanically removed carbonate fragments collected in the flow-through chamber (1 h) as well as a long-term collection method (1 wk) generally yielded comparable estimates for the capacity of these sponges to mechanically remove substratum. Observed interspecific variation could evidently be linked to the adopted boring strategy (i.e. gallery-forming, cavity-forming or network-working) and presence or absence of symbiotic zooxanthellae. Notably, a clear diurnal pattern was found only in species that harbour a dense photosymbiotic community. In these species chemical erosion was substantially higher during the day. Overall, the sum of individually acquired chemical and mechanical erosion using flow-through incubations was comparable to rates obtained gravimetrically. Such consistency is a first in this field of research. These findings support the much needed confirmation that, depending on the scientific demand, the different approaches presented here can be implemented concurrently as standardized methods.

The positive effect of biodiversity : Using root traits to understand effects of plant diversity and drought on grassland productivity
Bakker, Lisette Marleen - \ 2018
University. Promotor(en): Liesje Mommer, co-promotor(en): Jasper van Ruijven. - Wageningen : Wageningen University - ISBN 9789463437622 - 201
Nominaties : genomineerden Ekoland Innovatieprijs biologische landbouw 2018
Boxtel, M. van; Veluw, K. van; Schlaman, G. - \ 2018
Ekoland (2018)1. - ISSN 0926-9142 - p. 10 - 13.
De jury van de Ekoland Innovatieprijs 2018 bestaat uit Gea Bakker, Maria van Boxtel, Geertje Schlaman, Bart Fokkens, Lex Kruit en Kees van Veluw. De bedrijven werden vervolgens beoordeeld op de criteria innovatie, originaliteit, effectiviteit, algemene toepasbaarheid, maatschappelijke acceptatie en duurzaamheid. Uit de door de lezers van Ekoland aangemelde dertien kandidaten heeft de jury uiteindelijk drie bedrijven geselecteerd. Innovaties in automatisering, productie- en kostenbeheersing en een nauwkeurige afstemming tussen teelt, verwerking en aflevering maakten veel indruk op de jury.
Complex dynamics in the uptake of new farming practices : a case study for organic waste application
Groeneveld, Anouschka ; Bakker, Martha ; Peerlings, Jack ; Heijman, Wim - \ 2018
Journal of Environmental Planning and Management (2018). - ISSN 0964-0568 - 25 p.
economies of scale - innovation - learning - regime shift - social norm

Adverse environmental effects of intensive agriculture, together with scarcity in phosphates and water, urge farmers to find more sustainable practices. An example of such a sustainable practice is on-farm processing of organic waste. This paper explores three mechanisms that can lead to a widespread uptake of this technique: (1) economies of scale, (2) information sharing, and (3) adjustment of social norms. Although each of these mechanisms has been studied before, this paper provides new insights by considering the interactions that might exist between the different mechanisms when they are applied to real-life situations. Based on a pilot study, we developed a multi-criteria mathematical programming model at individual farm level. We used this model to simulate the uptake of on-farm processing of organic waste, as a result of the three mechanisms and their interactions. Our results show that each mechanism results in an increased uptake, but is not likely to cause a widespread uptake. Interaction between the mechanisms, will lead to a much higher uptake. This result suggests that simultaneous consideration of multiple mechanisms is essential to understand the behaviour of social–ecological systems.

De Eest in Nagele is proeflocatie voor bewaaronderzoek
Bakker, Pierre - \ 2018
Quantitative studies on potato genotypes and fodder radish varieties resistant to the rootknot nematode Meloidogyne chitwoodi
Teklu, Misghina Goitom - \ 2018
University. Promotor(en): Jaap Bakker, co-promotor(en): Thomas Been. - Wageningen : Wageningen University - ISBN 9789463437493 - 154
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