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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Cognitive and Affective Predictors of Illinois Residents’ Perceived Risks from Gray Wolves
Landon, A. ; Jacobs, M.H. ; Miller, C.A. ; Vaske, J.J. ; Williams, B. - \ 2019
Society & Natural Resources (2019). - ISSN 0894-1920 - 20 p.
Increasing wolf populations are a concern for wildlife managers inthe Midwestern U.S. Understanding the psychological mechanismsthat contribute to public perceptions of risk will enable developmentof strategies that seek to mitigate these risks, and suggest where outreach efforts may facilitate acceptance of wolves. We examined the psychological factors that influence Illinois residents’ perceived risks from wolves. We hypothesized that individuals’ perceived risks from wolves were a function of their attitudes toward wolves, negative affect toward wolves, and basic beliefs about wildlife. Data were obtained from a survey of the Illinois public (n¼784). Negative affect and attitudes toward wolves were direct predictors of perceived risks. Basic beliefs predicted attitudes and negative affect toward wolves. Negative affect predicted attitudes. Basic beliefs had direct and indirect effects on perceived risks.
Loss rates of honey bee colonies during winter 2017/18 in 36 countries participating in the COLOSS survey, including effects of forage sources
Gray, Alison ; Brodschneider, Robert ; Adjlane, Noureddine ; Ballis, Alexis ; Brusbardis, Valters ; Charrière, Jean Daniel ; Chlebo, Robert ; F. Coffey, Mary ; Cornelissen, Bram ; Amaro da Costa, Cristina ; Csáki, Tamás ; Dahle, Bjørn ; Danihlík, Jiří ; Dražić, Marica Maja ; Evans, Garth ; Fedoriak, Mariia ; Forsythe, Ivan ; Graaf, Dirk de; Gregorc, Aleš ; Johannesen, Jes ; Kauko, Lassi ; Kristiansen, Preben ; Martikkala, Maritta ; Martín-Hernández, Raquel ; Medina-Flores, Carlos Aurelio ; Mutinelli, Franco ; Patalano, Solenn ; Petrov, Plamen ; Raudmets, Aivar ; Ryzhikov, Vladimir A. ; Simon-Delso, Noa ; Stevanovic, Jevrosima ; Topolska, Grazyna ; Uzunov, Aleksandar ; Vejsnaes, Flemming ; Williams, Anthony ; Zammit-Mangion, Marion ; Soroker, Victoria - \ 2019
Journal of Apicultural Research 58 (2019)4. - ISSN 0021-8839 - p. 479 - 485.
Apis mellifera - beekeeping - citizen science - colony winter losses - forage sources - monitoring - mortality - survey

This short article presents loss rates of honey bee colonies over winter 2017/18 from 36 countries, including 33 in Europe, from data collected using the standardized COLOSS questionnaire. The 25,363 beekeepers supplying data passing consistency checks in total wintered 544,879 colonies, and reported 26,379 (4.8%, 95% CI 4.7–5.0%) colonies with unsolvable queen problems, 54,525 (10.0%, 95% CI 9.8–10.2%) dead colonies after winter and another 8,220 colonies (1.5%, 95% CI 1.4–1.6%) lost through natural disaster. This gave an overall loss rate of 16.4% (95% CI 16.1–16.6%) of honey bee colonies during winter 2017/18, but this varied greatly from 2.0 to 32.8% between countries. The included map shows relative risks of winter loss at regional level. The analysis using the total data-set confirmed findings from earlier surveys that smaller beekeeping operations with at most 50 colonies suffer significantly higher losses than larger operations (p <.001). Beekeepers migrating their colonies had significantly lower losses than those not migrating (p <.001), a different finding from previous research. Evaluation of six different forage sources as potential risk factors for colony loss indicated that intensive foraging on any of five of these plant sources (Orchards, Oilseed Rape, Maize, Heather and Autumn Forage Crops) was associated with significantly higher winter losses. This finding requires further study and explanation. A table is included giving detailed results of loss rates and the impact of the tested forage sources for each country and overall.

Shallow Cumulus Representation and Its Interaction with Radiation and Surface at the Convection Gray Zone
Pedruzo-Bagazgoitia, Xabier ; Jiménez, Pedro A. ; Dudhia, Jimy ; Vilà-Guerau De Arellano, Jordi - \ 2019
Monthly Weather Review 147 (2019)7. - ISSN 0027-0644 - p. 2467 - 2483.
This study presents a systematic analysis of convective parameterizations performance with interactive radiation, microphysics, and surface on an idealized day with shallow convection. To this end, we analyze a suite of mesoscale numerical experiments (i.e., with parameterized turbulence). In the first set, two different convection schemes represent shallow convection at a 9-km resolution. These experiments are then compared with model results omitting convective parameterizations at 9- and 3-km horizontal resolution (gray zone). Relevant in our approach is to compare the results against two simulations by different large-eddy simulation (LES) models. Results show that the mesoscale experiments, including the 3-km resolution, are unable to adequately represent the timing, intensity, height, and extension of the shallow cumulus field. The main differences with LES experiments are the following: a too late onset, too high cloud base, and a too early transport of moisture too high, overestimating the second cloud layer. Related to this, both convective parameterizations produce warm and dry biases of up to 2 K and 2 g kg−1, respectively, in the cloud layer. This misrepresentation of the cloud dynamics leads to overestimated shortwave radiation variability, both spacewise and timewise. Domain-averaged shortwave radiation at the surface, however, compares satisfactorily with LES. The shortwave direct and diffuse partition is misrepresented by the convective parameterizations with an underestimation (overestimation) of diffuse (direct) radiation both locally and, by a relative 40% (10%), of the domain average.
The potato cyst nematode effector RHA1B is a ubiquitin ligase and uses two distinct mechanisms to suppress plant immune signaling
Kud, Joanna ; Wang, Wenjie ; Gross, Rachel ; Fan, Youhong ; Huang, Li ; Yuan, Yulin ; Gray, Amanda ; Duarte, Aida ; Kuhl, Joseph C. ; Caplan, Allan ; Goverse, Aska ; Liu, Yongsheng ; Dandurand, Louise-Marie ; Xiao, Fangming - \ 2019
PLoS Pathogens 15 (2019)4. - ISSN 1553-7366 - 18 p.
Plant pathogens, such as bacteria, fungi, oomycetes and nematodes, rely on wide range of virulent effectors delivered into host cells to suppress plant immunity. Although phytobacterial effectors have been intensively investigated, little is known about the function of effectors of plant-parasitic nematodes, such as Globodera pallida, a cyst nematode responsible for vast losses in the potato and tomato industries. Here, we demonstrate using in vivo and in vitro ubiquitination assays the potato cyst nematode (Globodera pallida) effector RHA1B is an E3 ubiquitin ligase that employs multiple host plant E2 ubiquitin conjugation enzymes to catalyze ubiquitination. RHA1B was able to suppress effector-triggered immunity (ETI), as manifested by suppression of hypersensitive response (HR) mediated by a broad range of nucleotide-binding leucine-rich repeat (NB-LRR) immune receptors, presumably via E3-dependent degradation of the NB-LRR receptors. RHA1B also blocked the flg22-triggered expression of Acre31 and WRKY22, marker genes of pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI), but this did not require the E3 activity of RHA1B. Moreover, transgenic potato overexpressing the RHA1B transgene exhibited enhanced susceptibility to G. pallida. Thus, our data suggest RHA1B facilitates nematode parasitism not only by triggering degradation of NB-LRR immune receptors to block ETI signaling but also by suppressing PTI signaling via an as yet unknown E3-independent mechanism

Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Harmonization of methods of analysis for natural toxins in feed – Activities of CEN/TC 327/WG 5
Witsenburg, J. ; Bodi, Dorina ; Gray, K. ; Mulder, P.P.J. ; Stroka, J. ; Mol, J.G.J. - \ 2018
Volumetric gray matter measures of amygdala and accumbens in childhood overweight/obesity
Perlaki, Gabor ; Molnar, Denes ; Smeets, Paul A.M. ; Ahrens, Wolfgang ; Wolters, Maike ; Eiben, Gabriele ; Lissner, Lauren ; Erhard, Peter ; Meer, Floor van; Herrmann, Manfred ; Janszky, Jozsef ; Orsi, Gergely - \ 2018
PLoS ONE 13 (2018)10. - ISSN 1932-6203

Objectives Neuroimaging data suggest that pediatric overweight and obesity are associated with morphological alterations in gray matter (GM) brain structures, but previous studies using mainly voxel-based morphometry (VBM) showed inconsistent results. Here, we aimed to examine the relationship between youth obesity and the volume of predefined reward system structures using magnetic resonance (MR) volumetry. We also aimed to complement volumetry with VBM-style analysis. Methods Fifty-one Caucasian young subjects (32 females; mean age: 13.8±1.9, range: 10.2–16.5 years) were included. Subjects were selected from a subsample of the I.Family study examined in the Hungarian center. A T1-weighted 1 mm3 isotropic resolution image was acquired. Age- and sex-standardized body mass index (zBMI) was assessed at the day of MRI and ~1.89 years (mean±SD: 689±188 days) before the examination. Obesity related GM alterations were investigated using MR volumetry in five predefined brain structures presumed to play crucial roles in body weight regulation (hippocampus, amygdala, accumbens, caudate, putamen), as well as whole-brain and regional VBM. Results The volumes of accumbens and amygdala showed significant positive correlations with zBMI, while their GM densities were inversely related to zBMI. Voxel-based GM mass also showed significant negative correlation with zBMI when investigated in the predefined amygdala region, but this relationship was mediated by GM density. Conclusions Overweight/obesity related morphometric brain differences already seem to be present in children/adolescents. Our work highlights the disparity between volume and VBM-derived measures and that GM mass (combination of volume and density) is not informative in the context of obesity related volumetric changes. To better characterize the association between childhood obesity and GM morphometry, a combination of volumetric segmentation and VBM methods, as well as future longitudinal studies are necessary. Our results suggest that childhood obesity is associated with enlarged structural volumes, but decreased GM density in the reward system.

Money talk : How relations between farmers and advisors around financial management are shaped
Hilkens, Aniek ; Reid, Janet I. ; Klerkx, Laurens ; Gray, David I. - \ 2018
Journal of Rural Studies 63 (2018). - ISSN 0743-0167 - p. 83 - 95.
Agricultural advice - Agricultural entrepreneurship - Agricultural finance - Agricultural Knowledge and Innovation Systems (AKIS) - Dairy - Farm management - Farmer-advisor relationships - Financial management - Rural extension

The nature of interactions between farmers and advisors is the focus of a growing body of research. While many studies explore the potential role of advisors in facilitating farmers’ practice change in practices related to agricultural production such as soil, water, pest and animal health management, studies that specifically investigate how advisors support farmers with financial management (FM) are limited. The contribution this paper makes is to identify who farmers’ FM advisors are and to shed light on how farmer-advisor interactions about FM are shaped. Semi-structured interviews with both farmers and a range of advisors (bankers, accountants, farm management consultants, specialist financial advisors and industry funded advisors) were conducted. The main findings are that farm financial information and FM are considered to be sensitive topics and being good at FM is not central to farmers’ identity (relative to e.g. production management). Due to the sensitivity and taboo around the topic and the low level of interest in FM, most farmers do not actively seek to acquire financial advice. Farmers most openly discuss FM with their banker and accountant and some seek advice from farm management consultants. Advice seeking from other advisors was limited. Theoretical implications are that FM as a topic of advice introduces unique dynamics to interactions between farmer and advisor, which highlights the importance of better consideration of taboo and sensitive topics in advisory interactions. Furthermore, the findings on how the bankers’ authority impacts on the advisory relationship with farmers indicated that issues of power in view of such authoritative advisory relationships need to be better considered. To enhance effective provisioning on FM advice, policy could focus on improving the match between demand and supply, and help create awareness about the importance of discussing FM to reduce the sensitivity of the topic.

Regulating food fraud : Public and private law responses in the EU, Italy and the Netherlands
Corini, Antonia ; Meulen, Bernd van der - \ 2018
In: A Handbook of Food Crime / Gray, Allison, Hinch, Ronald, Policy Press - ISBN 9781447336013 - p. 159 - 174.
What We Know about Software Test Maturity and Test Process Improvement
Garousi, Vahid ; Felderer, Michael ; Hacaloglu, Tuna - \ 2018
IEEE Software 35 (2018)1. - ISSN 0740-7459 - p. 84 - 92.
multivocal literature review - software development - software engineering - software testing - systematic literature review - test maturity - test maturity assessment - Test Maturity Model Integration - test process assessment - test process improvement - TMA - TMMi - TPI
In many companies, software testing practices and processes are far from mature and are usually conducted in an ad hoc fashion. Such immature practices lead to negative outcomes - for example, testing that doesn't detect all the defects or that incurs cost and schedule overruns. To conduct test maturity assessment (TMA) and test process improvement (TPI) systematically, researchers and practitioners have proposed various approaches and frameworks. Motivated by a recent industrial project in TMA and TPI and wanting to identify the state of the art and practice in this area, researchers conducted a review of both the scientific literature and practitioners' gray literature (for example, blog posts). The review identified 58 test maturity models and many sources with varying degrees of empirical evidence. The review's results can serve as an evidence-based overview of and index to the vast body of knowledge in this important, fast-growing area. Using this knowledge, both researchers and practitioners should be able to assess and improve the maturity of test processes.
Valorisation of waste streams from by-product to worm biomass
Laarhoven, Bob - \ 2017
Wageningen University. Promotor(en): C.J.N. Buisman, co-promotor(en): B.G.. Temmink; H.J.H. Elissen. - Wageningen : Wageningen University - ISBN 9789463438117 - 141
biomass - residual streams - animal nutrition - fisheries - organic wastes - helminths - biomassa - reststromen - diervoeding - visserij - organisch afval - wormen

There is a global demand for more feed resources to keep up with the increasing production of livestock. The hunger for resources is most urgent in the aquaculture sector, which to a large degree depends on the non-sustainable use of fish oil/ meal from wild fish. Aquatic macro invertebrates such as the freshwater worm Lumbriculus variegatus (Oligochaeta, Lumbriculidae, common name blackworms, further abbreviated as Lv) are rich in proteins, lipids, vitamins and minerals. When cultivated on safe and low-grade organic wastes they can provide a sustainable fishmeal alternative for most freshwater and marine fish.

Chapter 1 introduces the concept of aquatic worm production on waste streams. Worm biomass composition and relevant research lines are explained. Organic waste sludges from food industries are a rich source of bio-molecules and can be upgraded to (fish) feed when fed to aquatic worms. For valorisation of waste streams by aquatic worms, as proposed in this thesis, these streams preferably are free from contaminants such as organic micro pollutants, heavy metals and pathogens. For example, this would not be the case when sewage (municipal) sludge is used as a substrate for the worms. However, such contaminated sludges may still be applied for non-food applications. Thus, the quality of the waste stream that is used as a substrate for the worms determines the application potential of the worm biomass as well as the options for downstream processing and refinery.

Previous research showed that Lv can be used for reduction and compaction of sewage sludge. The consumption of (suspended) sludge particles results in a dry matter reduction of 25 - 50 % and in worm faeces that are 60 % more compact than the original waste sludge. This contributes to a significant reduction in sludge processing costs. Sludge reduction by aquatic worms is mainly studied by research groups in The Netherlands and in China. Unfortunately, it is generally accepted free swimming worms in full-scale wastewater treatment plants is extremely difficult, mainly because of large (seasonal) population fluctuations. A controlled reactor concept applying the sessile (crawling, sediment dwelling) species Lv already was developed in earlier research. The key characteristic of this reactor is a carrier material for the worms, which also functions as a separation layer between the waste stream (worm food) and a water phase used for aeration, worm harvesting and worm faeces collection. This concept also was the starting point for the development of the improved reactor concept that is described in this thesis.

The two main objectives of this thesis were: (1) to assess the potential of organic waste streams and by-products for Lv production for fish feed and (2) to develop a (cost and resource) effective bioreactor for this purpose.

In Chapter 2 a new, standardized method is described and tested that can be used for a quantitative and qualitative assessment of the effect of different substrates on worm growth. This method not only can be used to select waste streams suitable for worm production, but also is proposed as a tool is ecotoxicology studies.

The test method consists of beaker experiments with a combination of agar and sand to optimize food uptake by and growth of the worms. The effects of agar gel, sand, and food quantity were studied and evaluated for different food sources. Agar gel addition ameliorated growth conditions by reducing microbial food hydrolysis and by improving the sediment structure. This guaranteed that substrate ingestion and worm growth in the first place were the result of the food quality and the effect of other (environmental) factors was reduced. A final test with secondary potato starch sludge demonstrated the test method is appropriate for the evaluation of solid and suspended organic feedstuffs/waste streams.

In Chapter 3 the standardized method of chapter 2 was used for worm growth studies, focussing on the effect of carbon to nitrogen (C/N) ratios of diets on worm growth and reproduction. Growth and reproduction of Lv on different combinations of wheat based derivatives like gluten and gray starch was studied at fixed isoenergetic levels (expressed as chemical oxygen demand (COD) of the food), but at different C/N ratios. Growth and reproduction rates were compared to those on Tetramin, a substrate known to result in excellent worm growth. Growth was mainly controlled by the C/N ratio of the single and mixed wheat fraction diets. Lower C/N ratios of around 6-7 gave a much better performance than high C/N ratios of around 20. This probably was caused by Lv relying on the presence of proteins as carbon and energy source. Although growth and reproduction rates were not as high as on the control diet, the results were promising for development of a worm biomass production reactor, operating on by-products from wheat processing industries.

In Chapter 4 a new reactor concept for Lv cultivation on waste streams was developed and tested. In a vertical tubular reactor a centralized food compartment was surrounded by a gravel layer that mimicked the natural habitat of Lv. Secondary (biological) sludge from a potato starch processing industry was used as a clean and low value food source. The results with respect to worm growth rate, density and production and nutrient recovery were compared to the previous reactor design. Much higher worm densities were achieved (6.0 compared to 1.1 kg ww m-2 carrier material) as well as much faster Lv growth rates (4.4 - 12 compared to 1.2 % d-1). As a result the areal worm production rate was no less than 40 times higher (560 compared to 14 g ww m-2 d-1). The higher worm density, which was found to be independent of gravel size in a range of 2.4 to 8.0 mm, allowed for a significantly shorter food retention time in the reactor (~ 2.2 days compared to > 10 days for the previous reactor design). This restricted microbial mineralization of the food, making high nutrient recoveries from waste to worm biomass possible: 16-30 % COD, 19-22 % N and 9-11 % P. The high biomass density also limited the release of ammonium, which at large concentrations is toxic for the worms. However, even shorter food retention times (e.g. higher loading rates) are not recommended as a minimum microbial activity is needed for conversion of the original substrate into compounds that can be taken up by the worms.

In Chapter 5 worm growth, reproduction and biomass quality were evaluated on several waste streams and by-products of bacterial, animal and plant origin. The effect of 26 different diets, all applied at high food levels, on Lv growth, reproduction and fatty acid (FA) content and profile were investigated. For this purpose the standardized test method of Chapter 2 was used. In addition, it was discussed which diet composition and food sources would be most suitable for large scale production of Lv.

Diets consisting of single cell biomass from bacterial or plant origin with a high protein content (C/N ratio < 8.8), high P content (C/P < 50) and low in total ammonia nitrogen (TAN) (< 20 g N/kg) gave the highest growth rates and vital worms without signs of mortality. Besides the C/P ratio of the diet, worm conditions related with the difference between test and pre-culture conditions. The starting weight of the worms seemed to have an effect on the total fatty acid content of the worms. The growth potential of a diet rich in proteins and P depends on how much TAN is associated with the diet. By blending different food sources these factors to a certain extent can be manipulated. Lv seemed to have a distinct and very stable FA composition, irrespective of the diet’s FA composition. The worms were rich in poly unsaturated FAs (PUFAs), including several w3 and w6 FAs, and contained relatively high levels of C18 and C20 PUFAs. This makes them suitable as fish feed, in particular for freshwater fish.

In order to serve aquaculture feed markets with an attractive alternative to fish meal, such as aquatic worm biomass, a continuous and secure bulk production needs to be realized. In Chapter 6 the performance parameters established in chapter 4 (worm growth rate, density and biomass production rate) were used as the input for a feasibility assessment of large scale worm production on secondary sludge from the potato industry. In addition, in chapter 6 future value chains and lines of research were discussed.

A hypothetical worm production system treating the surplus secondary sludge from a potato processing factory can reduce excess sludge production by 50 % in solids and 62 % in volume. This is accompanied by a daily production of 1.6 metric ton of fresh worm biomass. With a very conservative estimation of the worm density of 1.6 kg ww/m2 carrier material a footprint of the system of 217 m2 can be realized, which is at least two times smaller than with a previous reactor design without a gravel layer. With reduced sludge processing costs and a conservative market price of 1.4 €/kg dry worm biomass, worm production can already be realized at an annual rate of return of 3 years. However, the costs are highly sensitive for worm biomass stocking, reactor construction and operation. A more accurate economic assessment should be based on the results of pilot-scale research.

Two general product types, whole biomass (as fish feed) and refined products can be distinguished and applied in two application areas (feed and non-food), depending on the quality of the organic (waste) sludge that the worms have been produced from. Valorisation for potential bulk markets needs further refinery of crude worm biomass into a lipid (worm oil) and a protein fraction (protein isolate). This can result in several new and unique business models in aquaculture, feed, chemical and agriculture sectors. Obviously, an assessment of economical and legislative boundary conditions needs to be part of such business models.

Worm biomass is a potential high quality fishmeal replacer, with a similar or even better potential than other waste based alternatives such as single cell biomass and insects. A comparison between Lv and fishmeal with respect to crude composition, essential amino acids and FAs learns that Lv is a highly suitable fish feed source. It can provide essential amino acids at sufficiently high levels. Based on its FA composition and (relatively low) fat content, Lv can best be considered a protein source. Still, worm biomass is rich in PUFA, which could be a potential high value product for feed applications. Compared to black soldier fly and bacterial production systems, Lv shows intermediate production efficiencies, while biomass harvesting and processing probably is more easy.

Additional advantages of Lv worm biomass to replace fishmeal are: 1) Lv acts as a strong natural fish attractant, 2) the growth efficiency of fish on worms is high in comparison to regular feeds, 3) the nutritional profile of worms matches that of fishmeal, 4) the worms are a natural feed source for freshwater fish and 5) the worms allow a secure and stable feed production that is independent of natural resources.

Further recommendations for future research as outlined and discussed in chapter 6 are mostly related to the technical upscaling of the reactor technology and obtaining more detailed insight in controlled worm growth in response to food characteristics, reactor design and operational conditions.

Speaker in the keynote panel for the IACM Lifetime Achievement Award of Prof. Barbara Gray
Dewulf, Art - \ 2017
Unraveling the genetics of Botrytis cinerea resistance in Gerbera hybrida
Fu, Yiqian - \ 2017
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): P.F.P. Arens; J.M. van Tuyl. - Wageningen : Wageningen University - ISBN 9789463431811 - 159
gerbera - plant pathogenic fungi - botrytis cinerea - disease resistance - genetic mapping - transcriptomics - quantitative trait loci - plant breeding - gerbera - plantenziekteverwekkende schimmels - botrytis cinerea - ziekteresistentie - genetische kartering - transcriptomica - loci voor kwantitatief kenmerk - plantenveredeling

Gerbera hybrida is one of the top five cut flowers. It is well-known to people for its variation in flower color and patterning. Gerbera breeding at the moment is done using conventional methods which are based on a phenotypic selection. This has drawbacks in breeding speed and efficiency, especially for complex traits like disease resistance. Gerbera gray mold, promoted by high humidity during the production in greenhouses or by an accumulation of condensate during transportation, is a considerable threat to the gerbera production. Gerbera gray mold is caused by Botrytis cinerea and plant resistance to B. cinerea is considered to be a polygenic trait that needs the contribution of multiple loci, and on top of that is highly affected by the environment. Conventional breeding might be inefficient for improving Botrytis resistance in gerbera.

In this study, the transcriptomes of four parents of two gerbera populations were sequenced using Illumina paired-end sequencing. Transcriptome data provides a resource for genetic dissection and an insight to explore gene functions for this ornamental crop. To identify the QTL regions leading to the phenotypic variation in Botrytis resistance, and establishing a relationship between marker genotype and phenotypic variation for marker assisted selection (MAS), genetic linkage maps were constructed with SNP markers in the two F1 segregating populations. A total of 20 QTLs were identified in the parental maps of the two populations. The number of QTLs found and the explained variance of most QTLs detected reflects the complex mechanism of Botrytis disease response. Narrowing down the QTL region and identifying the causal gene(s) underlying a QTL could maximize the effective use of MAS in breeding. Homologs of known functional genes involved in Botrytis resistance from other species were obtained in gerbera and SNP markers identified and mapped. Twenty-nine candidate genes were mapped and seven candidate genes could be mapped on both populations. Seven candidate genes were located in the vicinity of the QTLs detected. The co-localization of QTLs with CGs gives an indication that these candidate genes could probably be involved in resistance to Botrytis and provide a more precise possibility to use MAS in gerbera breeding in the future. A tobacco rattle virus (TRV) based gene silencing system which was used to inspect the function of two candidate genes. The two CGs are the homologs of the genes responsible for Botrytis resistance in tomato and both mapped in QTL regions related to Botrytis resistance in gerbera ray floret test. Silencing the two genes by VIGS, showed smaller lesion sizes upon Botrytis infection on gerbera ray florets compared with the controls.

The entire research went from the generation of four parental transcriptome data sets to development of SNP markers (Chapter 2), construction of genetic maps and to mapping QTLs for Botrytis resistance (Chapter 3). This was further on combined with candidate gene searching in other crops, querying and mapping homologous genes (Chapter 4) and characterizing the candidate genes which co-localized with QTLs (Chapter 5). The whole process not only helped us to unravel the genetics of Botrytis resistance in gerbera and develop genetic tools for gerbera improvement, but also could serve as guidance for developing marker-assisted selection for other ornamental plants from the beginning.

Doing Whole Earth justice : a reply to Cafaro et al.
Büscher, Bram ; Fletcher, Robert ; Brockington, Dan ; Sandbrook, Chris ; Adams, Bill ; Campbell, Lisa ; Corson, Catherine ; Dressler, Wolfram ; Duffy, Rosaleen ; Gray, Noella ; Holmes, George ; Kelly, Alice ; Lunstrum, Elizabeth ; Ramutsindela, Maano ; Shanker, Kartik - \ 2017
Oryx 51 (2017)3. - ISSN 0030-6053 - p. 401 - 401.
Onset and duration of gray seal (Halichoerus grypus) molt in the Wadden Sea, and the role of environmental conditions
Schop, Jessica ; Aarts, Geert ; Kirkwood, Roger ; Cremer, Jenny S.M. ; Brasseur, Sophie M.J.M. - \ 2017
Marine Mammal Science 33 (2017)3. - ISSN 0824-0469 - p. 830 - 846.
Halichoerus grypus - Annual life cycle - Dutch Wadden Sea - Gray seals - Haul-out - North Sea - Peak molt - Phocid seals - Population monitoring

Surveys of gray seals (Halichoerus grypus) during the molt period, when they are abundant on land, can be used to monitor changes in population size, but accurate interpretation of results requires an understanding of the molt process and how it may vary between years. This study investigates variability in onset (start date) and duration of visible molt by gray seals in the Wadden Sea, and the influence of environmental conditions on the onset. Molt was monitored in nine captive seals and observed molt phases were applied to wild seals over seven annual molt periods between 2004 and 2010, monitored using aerial photography. The onset of visible molt varied significantly between years, for example it differed 28 d between 2008 and 2009. Model selection by AIC retained one environmental variable that correlated with molt onset; however, its effect was inconsistent within the molt season and did not explain some of the apparent observed annual variation. Hence, the main causes of interannual variability in the onset of molt remain unclear and warrant further study. Researchers should account for annual variability in the onset of molt when interpreting survey results based on molt counts.

Half-Earth or Whole Earth? Radical ideas for conservation, and their implications
Büscher, Bram ; Fletcher, Robert ; Brockington, Dan ; Sandbrook, Chris ; Adams, William M. ; Campbell, Lisa ; Corson, Catherine ; Dressler, Wolfram ; Duffy, Rosaleen ; Gray, Noella ; Holmes, George ; Kelly, Alice ; Lunstrum, Elizabeth ; Ramutsindela, Maano ; Shanker, Kartik - \ 2017
Oryx 51 (2017)3. - ISSN 0030-6053 - p. 407 - 410.
Biodiversity - economy - Half-Earth - inequality - protected area

We question whether the increasingly popular, radical idea of turning half the Earth into a network of protected areas is either feasible or just. We argue that this Half-Earth plan would have widespread negative consequences for human populations and would not meet its conservation objectives. It offers no agenda for managing biodiversity within a human half of Earth. We call instead for alternative radical action that is both more effective and more equitable, focused directly on the main drivers of biodiversity loss by shifting the global economy from its current foundation in growth while simultaneously redressing inequality.

Hanseniaspora uvarum prolongs shelf life of strawberry via volatile production
Qin, Xiaojie ; Xiao, Hongmei ; Cheng, Xu ; Zhou, Hailian ; Si, Linyuan - \ 2017
Food Microbiology 63 (2017). - ISSN 0740-0020 - p. 205 - 212.
Antagonistic yeast - Bio-fumigation - Botrytis cinerea - Hanseniaspora uvarum - Strawberry - Volatile organic compounds

Gray mold caused by Botrytis cinerea led to severe postharvest losses for strawberry industry. In recent years, some studies have shown that postharvest diseases of strawberry can be controlled by using bacterial, fungal and yeast strains. The yeast strain Hanseniaspora uvarum was shown as an effective antagonist against B. cinerea growth. Here, we further investigated the volatile organic compounds (VOCs) production of H. uvarum and how this could impact on postharvest gray mold control of strawberry. A total of 28 VOCs were detected by GC-MS in the headspace of H. uvarum and strawberry with/without B. cinerea (SI and RSI ≥800). Among these VOCs, 15 VOCs were detected in both conditions, 4 VOCs were H. uvarum and strawberry without B. cinerea and the other 9 VOCs were only detected when B. cinerea was inoculated. Two VOCs, ethyl acetate and 1,3,5,7-cyclooctatetraene, enhanced by inoculation of B. cinerea. In in vitro assay, H. uvarum significantly inhibited mycelial growth and spore germination of B. cinerea via VOCs production. Moreover, in vivo assay showed that H. uvarum reduced B. cinerea infection of strawberry and maintained fruit appearance, firmness and total soluble solids via VOCs production. Collectively, our results showed that H. uvarum VOCs significantly controlled postharvest gray mold of strawberry and prolonged the storage time and shelf life.

Investigation of oral gels breakdown using image analysis
Tournier, Carole ; Devezeaux de Lavergne, Marine ; Velde, Fred van de; Stieger, Markus ; Salles, Christian ; Bertrand, Dominique - \ 2017
Food Hydrocolloids 63 (2017). - ISSN 0268-005X - p. 67 - 76.
Emulsion-filled gels - Food bolus - Image texture analysis - Mastication - Mathematical morphology

Characterizing the dynamics of food oral breakdown is of interest to understand the temporal perception of food products. The present work aimed at studying the possible contribution of artificial vision for studying bolus formation. Four emulsion-filled gels were prepared from two concentrations of agar and gelatin. By combining two different layers of these gels, four samples of homogeneous composition and 6 samples of heterogeneous composition were prepared. The layers were colored independently in order to study their breakdown and mixing during oral processing. Images of spat out boluses were collected at different stages of the chewing process and studied by different image analysis methods: gray-level histograms, histogram of shape area, mathematical morphology and gray level co-occurrence matrix. Methods were compared for their ability in discriminating boluses as function of homogeneous gel composition and mastication time. Three methods were found to be relevant and mathematical morphology provided the best results. Using this method, we further analyzed the impact of heterogeneous gels composition on the evolution of boluses properties. Results showed that when two gel layers of different composition were combined, the agar layer dominated bolus properties and that the presence of gelatin impacted the dynamics of gel breakdown. The results were in agreement with results obtained previously when characterizing the physical properties of the boluses. This study showed that artificial vision provides reliable tools for evaluating the dynamics of bolus formation, which is complementary to the methods commonly used in literature while avoiding extensive manipulation of boluses.

FCMs as a common base for linking participatory products and models
Vliet, M. Van; Flörke, M. ; Varela-Ortega, C. ; Çakmak, E.H. ; Khadra, R. ; Esteve, P. ; D’Agostino, D. ; Dudu, H. ; Bärlund, I. ; Kok, K. - \ 2016
In: Environmental Modeling with Stakeholders / Gray, S., Paolisso, M., Jordan, R., Gray, S., Springer International Publishing - ISBN 9783319250519 - p. 145 - 169.
Fuzzy cognitive maps - Mathematical model - Participation - Stakeholder - System dynamics

Stakeholder involvement in modeling studies is increasing. Fuzzy Cognitive Maps (FCMs) are emerging as a promising tool to provide a common base for stakeholders and modelers. FCMs developed by stakeholders from three local Mediterranean case studies are used to construct a stakeholder based FCM. This is done via a workshop in which the locally developed FCMs are merged by regional experts. Graphs and quasi-dynamic output are then compared with an FCM based on a mathematical model (WaterGAP). This model-based FCM was developed in a small workshop by WaterGAP modelers, based on their knowledge of the model. Results show that FCMs indeed have the ability to serve as a common base for linking participatory products and models. The quasi-dynamic output helps to get a better understanding of the commonalities and differences in the two system descriptions. The comparisons showed that FCM is a very promising tool for linking stakeholders and modelers. It can function as a common base for comparison and to illustrate differences between stakeholder perceptions and models in detail. The system dynamics of FCMs can play an important role in the comparison between system perspectives and the dissemination process.

Flexible robotic systems for automated adaptive packaging of fresh and processed food products. Report on the deliverable 10.3 The Workshops (September 30th 2016) : GRANT AGREEMENT Number 311987
Gray, John ; Pekkeriet, E.J. - \ 2016
European Commission - 19 p.
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