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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Classifying fisher behaviour in The Netherlands: the potential of integrating fishing styles analysis into fleet behaviour models
Schadeberg, Amanda - \ 2019
Classifying fisher behaviour in The Netherlands: understanding fisher behaviour through mixed methods social science
Schadeberg, Amanda - \ 2019
On the use of in-silico simulations to support experimental design: A case study in microbial inactivation of foods
Garre, Alberto ; Peñalver-Soto, Jose Lucas ; Esnoz, Arturo ; Iguaz, Asunción ; Fernandez, Pablo S. ; Egea, Jose A. - \ 2019
PLoS ONE 14 (2019)8. - ISSN 1932-6203

The mathematical models used in predictive microbiology contain parameters that must be estimated based on experimental data. Due to experimental uncertainty and variability, they cannot be known exactly and must be reported with a measure of uncertainty (usually a standard deviation). In order to increase precision (i.e. reduce the standard deviation), it is usual to add extra sampling points. However, recent studies have shown that precision can also be increased without adding extra sampling points by using Optimal Experiment Design, which applies optimization and information theory to identify the most informative experiment under a set of constraints. Nevertheless, to date, there has been scarce contributions to know a priori whether an experimental design is likely to provide the desired precision in the parameter estimates. In this article, two complementary methodologies to predict the parameter precision for a given experimental design are proposed. Both approaches are based on in silico simulations, so they can be performed before any experimental work. The first one applies Monte Carlo simulations to estimate the standard deviation of the model parameters, whereas the second one applies the properties of the Fisher Information Matrix to estimate the volume of the confidence ellipsoids. The application of these methods to a case study of dynamic microbial inactivation, showing how they can be used to compare experimental designs and assess their precision, is illustrated. The results show that, as expected, the optimal experimental design is more accurate than the uniform design with the same number of data points. Furthermore, it is demonstrated that, for some heating profiles, the uniform design does not ensure that a higher number of sampling points increases precision. Therefore, optimal experimental designs are highly recommended in predictive microbiology.

Nitrogen and phosphorus constrain the CO2 fertilization of global plant biomass
Terrer, César ; Jackson, Robert B. ; Prentice, I.C. ; Keenan, Trevor F. ; Kaiser, Christina ; Vicca, Sara ; Fisher, Joshua B. ; Reich, Peter B. ; Stocker, Benjamin D. ; Hungate, Bruce A. ; Peñuelas, Josep ; McCallum, Ian ; Soudzilovskaia, Nadejda A. ; Cernusak, Lucas A. ; Talhelm, Alan F. ; Sundert, Kevin Van; Piao, Shilong ; Newton, Paul C.D. ; Hovenden, Mark J. ; Blumenthal, Dana M. ; Liu, Yi Y. ; Müller, Christoph ; Winter, Klaus ; Field, Christopher B. ; Viechtbauer, Wolfgang ; Lissa, Caspar J. Van; Hoosbeek, Marcel R. ; Watanabe, Makoto ; Koike, Takayoshi ; Leshyk, Victor O. ; Polley, H.W. ; Franklin, Oskar - \ 2019
Nature Climate Change 9 (2019). - ISSN 1758-678X - p. 684 - 689.

Elevated CO2 (eCO2) experiments provide critical information to quantify the effects of rising CO2 on vegetation1–6. Many eCO2 experiments suggest that nutrient limitations modulate the local magnitude of the eCO2 effect on plant biomass1,3,5, but the global extent of these limitations has not been empirically quantified, complicating projections of the capacity of plants to take up CO2 7,8. Here, we present a data-driven global quantification of the eCO2 effect on biomass based on 138 eCO2 experiments. The strength of CO2 fertilization is primarily driven by nitrogen (N) in ~65% of global vegetation and by phosphorus (P) in ~25% of global vegetation, with N- or P-limitation modulated by mycorrhizal association. Our approach suggests that CO2 levels expected by 2100 can potentially enhance plant biomass by 12 ± 3% above current values, equivalent to 59 ± 13 PgC. The global-scale response to eCO2 we derive from experiments is similar to past changes in greenness9 and biomass10 with rising CO2, suggesting that CO2 will continue to stimulate plant biomass in the future despite the constraining effect of soil nutrients. Our research reconciles conflicting evidence on CO2 fertilization across scales and provides an empirical estimate of the biomass sensitivity to eCO2 that may help to constrain climate projections.

Corrigendum: Exposure to antibiotics affects Saponin immersion-induced immune stimulation and shift in microbial composition in Zebrafish larvae
Nadal, Adrià López ; Peggs, David ; Wiegertjes, Geert F. ; Brugman, Sylvia - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X

In the original article, there was an error. The name of the transgenic line used was incorrect. The correct name of the line is "mpeg1:mCherry/mpx:eGFPi114" Corrections have been made to the Materials and Methods subsection Animals: "Adult Tg(mpeg1:mCherry/mpx:eGFPi114) (Renshaw et al., 2006; Bernut et al., 2014) zebrafish (kindly provided by Prof. Meijer, Leiden University), expressing mCherry under the macrophage-specific mpeg1 promotor and GFP under the neutrophil-specific mpx promotor were housed in Zebtec family tanks (Tecniplast, Buguggiate, Italy) under continuous flow-through at 28°C (14/10-hour light/dark cycle) at Carus facilities (WUR, Wageningen, Netherlands). Zebrafish were fed with a mixture of Artemia 230.000 npg (Ocean Nutrition Europe, Essen, Belgium) and Tetramin Flakes (Tetra, Melle, Germany) twice per day. Embryos were obtained by natural spawning and raised with E3 water (0.10 mM NaCl in demineralized water, pH 7.6) in petri dishes at 28°C (12/12-hour light/dark cycle) (Westerfield, 2007). Dead or fungus-infected embryos were identified by microscopy and discarded in tricaine/E3 solution [8.4% (v/v) 24 mM Tricaine (Sigma-Aldrich, DL, United States) stock solution in E3]. Larval ages are expressed in days post-fertilization (dpf). From 5 dpf onward larvae were fed with live daily cultured Tetrahymena pyriformis." Materials and Methods, subsection Dose-Response Experiment Saponin Exposure: "Double Tg(mpeg1:mCherry /mpx:eGFPi114) zebrafish larvae were randomly distributed in 6 well plates (n = 20 fish/well) and exposed to different concentrations [0, 0.5, 0.7 and 1.0 mg/ml] of saponin [ultrapure Soy Saponin 95%, kindly provided by Trond Kortner NMBU Oslo Norway, origin: Organic Technologies, Coshocton, OH (Krogdahl et al., 2015)] dissolved in the E3 (10 ml solution/well) from 6-9 dpf. Mortality was registered and all media were refreshed daily. At 24 h (7 dpf) and 72 h (9 dpf) after the start of the immersion, zebrafish (n = 6-11/group) were anaesthetized embedded and imaged using fluorescent microscopy (as described below). Per time point several larvae were euthanized for further analysis with an overdose MS-222 (8.4 ml of 24 mM Tricaine (Sigma-Aldrich, DL, United States) in 100 ml E3). Pools of 5 larvae were used for RNA extraction (3 pools per group at 24 h, 7-9 pools per group at 72 h) and gene expression was measured on cDNA by Real Time PCR (as described below). Two independent experiments were performed and data were combined." Materials and Methods, subsection Fluorescent in vivo imaging: "Tg(mpeg1:mCherry/mpx:eGFPi114) zebrafish larvae were anaesthetized with tricaine/E3 solution (4.2 ml of 24 mM Tricaine (Sigma-Aldrich, DL, United States) in 100 ml E3) and embedded in 1% low melting point agarose (Thermo Fisher Scientific, MA, United States). Larvae were imaged as whole mounts with a Leica M205 FA Fluorescence Stereo Microscope. After image acquisition, pictures were analyzed with ImageJ® software (United States National Institutes of Health, Bethesda, United States). The intestinal regions were manually selected per fish on the basis of the bright light picture and subsequently copied to the green and red channel pictures (Supplementary Figure S1). Within this intestinal region individual cells were counted for each fish. Furthermore, corrected total cell fluorescence (CTCF) was measured in ImageJ® on total fish larvae by using the following formula: Integrated density-(area of total fish x mean fluorescence of the background reading)." Material and Methods, subsection Experimental Design and Sampling Strategy Antibiotics and Saponin Exposure: A graphical representation of the experimental design and analysis performed per time-point is displayed in Figure 1. To assess the effect of antibiotics, 4 dpf Tg(mpeg1:mCherry/mpx:eGFPi114) fish were randomly distributed in five 6 well-plates (n = 20 fish/well) and 3 treatment conditions were established: (1) control (E3), (2) ciprofloxacin 5 μg/L (Sigma-Aldrich, DL, United States) or (3) oxytetracycline hydrochloride 5 μg/L (Sigma-Aldrich, DL, United States) (10 ml solution/well). The dose of antibiotics was based on several reviews and experimental papers summarizing environmental concentrations of antibiotics in water environments (Ding and He, 2010; Carvalho and Santos, 2016; Watts et al., 2017; Patrolecco et al., 2018; Zhou et al., 2018b) to be at a low dose (ng-μg/L range) and not acute dose (mg/L range). At 6 dpf, 4 pools of 5 larvae were sampled to assess changes in gene expression at baseline. Moreover, at 6 dpf DNA was isolated from 3 pools of 5 larvae to investigate microbiome composition at baseline. In vivo imaging was performed on n = 10 larvae/group to visualize innate immune cells. Subsequently, after sampling, at 6 dpf ultrapure soy saponin was applied to half of the remaining larvae at a concentration 0.5 mg/ml (to induce mild immune stimulation) so each treatment group was split into two, resulting in 6 treatment groups: (1) control, (2) ciprofloxacin (5 μg/L), (3) oxytetracycline hydrochloride (5 μg/L), (4) saponin (0.5 mg/ml), (5) ciprofloxacin + saponin (5 μg/L + 0.5 mg/ml), and (6) oxytetracycline hydrochloride + saponin (5 μg/L + 0.5 mg/ml). All treatment media were refreshed daily. At 9 dpf in vivo imaging was performed on n = 10 larvae/group to visualize innate immune cells. Gene expression was performed on 4 pools of 5 larvae to investigate immune gene expression and from 3 pools of 5 larvae DNA was isolated for microbiological analysis. Because of the error reported above, corrections have also been made to the Figure legends of Figure 2 and Figure 4. The correct legends appear below. Figure 2: Effect of saponin immersion on zebrafish larvae. (A) Percent survival of zebrafish exposed to control (E3), 0.5 mg/ml saponin, 0.7 mg/ml saponin and 1 mg/ml saponin from 6-9 dpf (n = 40 fish/treatment) (Log-rank Mantel-Cox Test for Chi-square, ∗∗∗p < 0.0005). (B) Representative pictures of the saponin-treated Tg(mpeg1:mCherry/mpx:eGFPi114) fish displaying green neutrophils and red macrophages. (C) Quantification of neutrophils and macrophages in the intestinal area (n = 6-11 fish/group) (one way ANOVA Kruskal-Wallis test with Dunn's Multiple comparison Post-Test, mean ± SEM, ∗p < 0.05 ∗∗p < 0.01). Top: counted cells in intestinal area. Bottom: Corrected Total Cell Fluorescence (CTCF, measure for total fluorescent pixels in the whole fish). Two independent experiments were performed and data are combined. Figure 4: Effect of antibiotic exposure on saponin-immune-stimulation. (A) Percent survival of zebrafish exposed to control (E3), ciprofloxacin (4-9 dpf) (5 ug/L) or oxytetracycline (4-9 dpf) (5 ug/ml) + /- saponin (0.5 mg/ml) from 6-9 dpf (n = 100 fish / treatment) (Log-rank Mantel-Cox Test for Chi-square). (B) Representative pictures of the antibiotic/saponin-treated Tg(mpeg1:mCherry/mpx:eGFPi114) fish displaying green neutrophils and red macrophages. (C) Quantification of neutrophils and macrophages in the intestinal area (n = 10 fish/ group) (one way ANOVA Kruskal-Wallis test with Dunn's Multiple comparison Post-Test, mean ± SEM, ∗p < 0.05). Two independent experiments were performed and one representative experiment is shown. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Effect of early life and current environmental enrichment and personality on attention bias in pigs
Luo, Lu ; Reimert, I. ; Haas, E.N. de; Kemp, B. ; Bolhuis, J.E. - \ 2019
In: Proceedings of the 53rd Congress of the International Society for Applied Ethology (ISAE). - Wageningen, The Netherlands : Wageningen Academic Publishers - ISBN 9789086863389 - p. 128 - 128.
Animals may show increased attention towards threatening stimuli when they are in a negativeaffective state, i.e. attention bias. A barren, stimulus-poor housing environment can inducestress and potentially a negative mood in pigs. Apart from current housing conditions, however,also the early life environment and personality characteristics might influence affective state.In this study, we aimed to investigate the effects of early life and current housing conditionsand personality (coping style) on attention bias in pigs. Pigs (n=128, 32 pens) housed inbarren or enriched housing in early life (B1 vs E1), experienced either a switch in housingconditions at 7 wks of age or not (creating B1B2, B1E2, E1E2 and E1B2 treatments). Theywere classified using a backtest as ‘high resister’ (HR, proactive coping style) or ‘low resister’(LR, reactive coping style) at 2 wks. Pigs were subjected to a 3-min attention bias test at 11wks of age. Half of the pigs were exposed to a 10-sec potential threat (T) and the other halfnot (C) in a test room with food in the centre. Attention towards the (location of the) threat,vigilance, eating and vocalisations were recorded. Firstly, behaviours of T and C pigs over thetest were compared. Secondly, for T pigs, effects of early life and current housing, coping styleand their interactions on behaviour during and for 150 sec after the threat were tested. Mixedmodels with random pen effects were used, except for squealing for which a Fisher’s exact testwas used. T pigs spent more time on vigilance behaviour (T: 13.6±1.4, C: 6.8±1.0%, P<0.001),less time on eating (T: 15.0±1.8, C: 27.8±2.4%, P<0.001), were more likely to squeal (T: 22%C: 6% of pigs, P<0.05) than C pigs, and paid more attention to the location of the threat (T:7.1±0.6, C: 0.5±0.1% of time, P<0.001) throughout the 3-min test, indicating that pigs didrespond to the threat. During presence of the threat, HR pigs showed more vigilance (P<0.05),particularly in E2 housing (E2-HR: 39.9±6.6, E2-LR: 6.7±2.9, B2-HR: 19.4±5.9, and B2-LR:12.1±4.4%, interaction P<0.05). E1-HR pigs (55.4±6.5%) tended to pay more attention to thethreat than E1-LR pigs (30.3±5.9%), with levels of B1-HR (46.4±6.8%) and B1-LR (48.3±7.6%)in between (interaction P<0.10). After presence of the threat, no effects of housing or copingstyle on vigilance, attention to location of the threat or eating were found. E2 pigs grunted moreoften than B2 pigs (9.6±1.7 vs 3.6±0.9 per min, P<0.01). E2 pigs were also more likely to squealthan B2 pigs (P<0.05), particularly the HR pigs (E2-HR: 50%, B2-HR: 0%, E2-LR: 21%, B2-LR:17%, interaction P<0.10). In conclusion, housing affected vigilance in a personality-dependentmanner during a short period of exposure to a potential threat. We found no strong effect ofearly life or current housing on attention bias after the threat, but current housing conditionsand personality did affect vocalisations.
Historical changes (1905-present) in catch size and composition reflect altering fisheries practices on a small Caribbean island
Vermeij, Mark J.A. ; Latijnhouwers, Kelly R.W. ; Dilrosun, Faisal ; Chamberland, Valérie F. ; Dubé, Caroline E. ; Buurt, Gerard van; Debrot, Adolphe O. - \ 2019
PLoS ONE 14 (2019)6. - ISSN 1932-6203

Effective assessments of the status of Caribbean fish communities require historical baselines to adequately understand how much fish communities have changed through time. To identify such changes and their causes, we compiled a historical overview using data collected at the beginning (1905-1908), middle (1958-1965) and end (1984-2016) of the 20th century, of the artisanal fishing practices and their effects on fish populations around Curaçao, a small island in the southern Caribbean. We documented historical trends in total catch, species composition, and catch sizes per fisher per month for different types of fisheries and related these to technological and environmental changes affecting the island's fisheries and fish communities. We found that since 1905, fishers targeted species increasingly farther from shore after species occurring closer to shore had become rare. This resulted in surprisingly similar catches in terms of weight, but not composition. Large predatory reef fishes living close to shore (e.g., large Epinephelid species) had virtually disappeared from catches around the mid-20th century, questioning the use of data from this period as baseline data for modern day fish assessments. Secondly, we compared fish landings to in-situ counts from 1969 to estimate the relative contributions of habitat destruction and overfishing to the changes in fish abundance around Curaçao. The decline in coral dominated reef communities corresponded to a concurrent decrease in the abundance and diversity of smaller reef fish species not targeted by fishers, suggesting habitat loss, in addition to fishing, caused the observed declines in reef fish abundance around Curaçao.

What is the best housing temperature to translate mouse experiments to humans?
Keijer, Jaap ; Li, Min ; Speakman, John R. - \ 2019
Molecular Metabolism 25 (2019). - ISSN 2212-8778 - p. 168 - 176.
Basal metabolic rate - Comparative physiology - Housing temperature - Human - Mouse - Thermoneutrality

Objectives: Ambient temperature impinges on energy metabolism in a body size dependent manner. This has implications for the housing temperature at which mice are best compared to humans. In 2013, we suggested that, for comparative studies, solitary mice are best housed at 23–25 °C, because this is 3–5 °C below the mouse thermoneutral zone and humans routinely live 3–5 °C below thermoneutrality, and because this generates a ratio of DEE to BMR of 1.6–1.9, mimicking the ratio found in free-living humans. Methods: Recently, Fischer et al. (2017) challenged this estimate. By studying mice at 21 °C and at 30 °C (but notably not at 23–25 °C) they concluded that 30 °C is the optimal housing temperature. Here, we measured energy metabolism of C57BL/6 mice over a range of temperatures, between 21.4 °C and 30.2 °C. Results: We observed a ratio of DEE to BMR of 1.7 at 27.6 °C and of 1.8 at 25.5 °C, suggesting that this is the best temperature range for housing C57BL/6 mice to mimic human thermal relations. We used a 24 min average to calculate the ratio, similar to that used in human studies, while the ratio calculated by Fisher et al. dependent on short, transient metabolic declines. Conclusion: We concur with Fisher et al. and others that 21 °C is too cool, but we continue to suggest that 30 °C is too warm. We support this with other data. Finally, to mimic living environments of all humans, and not just those in controlled Western environments, mouse experimentation at various temperatures is likely required.

Wild lobster (Panulirus ornatus) fry fishery in Balete bay, Davao Oriental : Catch trends and implications to fisheries management
Macusi, Edison D. ; Laya-Og, Manilyn E. ; Abreo, Neil Angelo S. - \ 2019
Ocean & Coastal Management 168 (2019). - ISSN 0964-5691 - p. 340 - 349.
Davao Oriental - Fisher's knowledge - Fisheries - Fry - Growth overfishing - Lobster fry - Mati City - Puerulus

The coastal ecosystem of the Philippines is one of the richest and most diverse on earth. Lobsters are one of the commercially exploited species targeted by small-scale fishers for their livelihood and income. This study aims to determine the catch, and catching pattern of the wild lobster fry fishery, quantify the catch per unit effort (CPUE) and identify issues and challenges present in the lobster fry fishery for improved conservation and management. A combination of semi-structured interviews (n = 90), focus group discussion (n = 35) and actual catch monitoring for three months of lobster fry fishers (n = 20) were conducted to elicit information on lobster catch, composition, fishing practices and issues and challenges. Results from the interview and focus groups showed that majority of fishers catch the fries of Panulirus ornatus, Parribacus antarcticus and Panulirus versicolor. They catch most of the lobster fries using bamboo traps and beach seine. The analysis of the CPUE also revealed significant results (P ≤ 0.05) with the good catch having the highest CPUE value (0.30 g) followed by the normal catch (0.16 g) and worst catch of (0.02 g). In terms of weekly field monitoring of the catches of 20 fishers, temporal variation in terms of weeks was highly significant (P = 0.000; R2 = 22). Some management issues mentioned by fishers include effluents from shrimp farming, illegal fishing, chemical residues from mango farms and improper waste disposal. The lack of a management plan, as well as a system to control who has access to the fishing ground of lobster fries, can negatively affect the long-term sustainability of the lobster fry fishery.

The development of a single-item Food Choice Questionnaire
Onwezen, M.C. ; Reinders, M.J. ; Verain, M.C.D. ; Snoek, H.M. - \ 2019
Food Quality and Preference 71 (2019). - ISSN 0950-3293 - p. 34 - 45.
Benefits - Construct - Food choice motives - Motivation - Reliability - Scale development - Single item measure - Validity
Based on the multi-item Food Choice Questionnaire (FCQ) originally developed by Steptoe and colleagues (1995), the current study developed a single-item FCQ that provides an acceptable balance between practical needs and psychometric concerns. Studies 1 (N = 1851) and 2 (2a (N = 3290), 2b (N = 4723), 2c (N = 270)) showed that the single-item FCQ scale has good convergent and discriminant validity. Generally, the results showed the highest correlations with the related multi-item dimensions (>0.40). Study 2 refined the scale. Only the items for convenience (Study 2a), sensory appeal (Study 2b) and mood (Study 2c) needed to be revised (as Study 1 showed a correlation between the multi-item and the single-item below the threshold of 0.60). The results also showed comparable predictive validity. Both methods revealed similar association patterns between food motives and consumption behaviours (Fisher's z tests revealed agreements of 86.2% for Study 1, 92.9% for Study 2a and 100% for Studies 2b and 2c). Study 3 (N = 6062) showed an example of the added value of a context-specific application for the single-item FCQ. Different motives were shown to be relevant across contexts, and the context-specific motives had additional explained variance beyond the general multi-item FCQ. Studies 2b and 3 also showed the performance of the single-item FCQ in an international context. In sum, the results indicate that the single-item FCQ can be used as a flexible and short substitute for the multi-item FCQ. The study also discusses the conditions that should be considered when using the single-item scale.
Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, M. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, V.G.A.A. ; Kamoun, Sophien - \ 2018
asexual reproduction - clonal lineage - Phytophthora infestans - emergent pathogen - evolution - immunity - phenotypic plasticity - expression polymorphism - structural variation - copy number variation - loss of heterozygosity
Background Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081–1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375–380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265–271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.
Classifying fisher behaviour in The Netherlands: a replication of the fishing styles method of Boonstra & Hentati-Sundberg (2016)
Schadeberg, Amanda - \ 2018
Precision phenotyping as a tool to automatically monitor health and welfare of individual animals housed in groups
Rodenburg, T.B. - \ 2018
In: Proceedings of the 52nd Congress of the International Society for Applied Ethology. - Wageningen, The Netherlands : Wageningen Academic Publishers - ISBN 9789086863228 - p. 134 - 134.
Farm animals are increasingly housed in large group housing systems. Monitoring health and welfare in these large groups can be challenging. In current welfare assessment schemes, attention for animal-based welfare indicators is increasing, resulting in a shi in focus from environment-based to animal-based indicators. However, in group settings monitoring these animal-based welfare indicators is challenging, especially at the level of the individual animal. Focusing on the individual level is relevant in many dierent settings, e.g. for precision feeding and management, or targeted veterinary care. Also, in the context of animal breeding, focus on the individual level is pivotal; this is frequently done by housing animals of potential interest for selection individually to measure (or evaluate) their phenotypes. In this way, however, no information about the performance of the individual in a group setting can be included in the breeding program, while social interactions can have profound eects on group performance. New genetic methodology now allows the modelling of these social interactions using direct and indirect genetic eects models. is type of methodology can for instance provide information on the propensity of an animal to become a victim of damaging behaviour (direct genetic eect), but also on the propensity to perform damaging behaviour (indirect genetic eect). To utilise this methodology, the ability to measure accurate individual phenotypes in a group setting becomes very important. Breeding companies currently have a strong interest in developing methods for precision phenotyping, relying on new technology that enables tracking of individuals using combinations of dierent sensors. is should allow the use of group housing in future breeding operations and should allow more accurate phenotyping. In the PhenoLab project, we investigated possibilities for tracking of location, activity and proximity of individual laying hens. To meet that aim, we tracked individual hens during a ve-minute Open Field test using two dierent tracking systems: Ultra-wideband tracking using TrackLab and automatic video tracking using EthoVision. Ultra-wideband tracking consists of an active RFID tag that is placed on the bird in a backpack. is tag is then located by triangulation by four beacons. Comparing distance moved between TrackLab and Ethovision yielded 96% similar results (sample of 24 hens). In a second step, the ultra-wideband tracking was also used to measure dierences in activity between high (HFP; n=45) and low (LFP; n=41) feather pecking lines of laying hens. e system was well able to detect the higher activity level in the HFP line compared with the LFP line (10 vs 5 m moving distance), that was also found in previous studies. Interestingly, within the HFP line, birds phenotyped as feather peckers using traditional video observations were found to be the most active individuals compared with the other phenotypes. Precision phenotyping technology could become an important tool to automatically monitor health and welfare of individual animals housed in groups.
Feather pecking phenotype affects behavioural responses of laying hens
Eijk, J.A.J. van der; Lammers, A. ; Rodenburg, T.B. - \ 2018
In: Proceedings of the 52nd Congress of the International Society for Applied Ethology. - Wageningen, The Netherlands : Wageningen Academic Publishers - ISBN 9789086863228 - p. 169 - 169.
Feather pecking (FP) is a major welfare and economic issue in the egg production industry. It involves hens pecking and pulling at feathers of conspecics, thereby negatively aecting welfare. Behavioural characteristics, such as fearfulness, have been related to FP. Although many studies have identied dierences in fearfulness between lines that dier in FP, the relationship between actual FP behaviour (i.e. FP phenotypes) and fearfulness is not well understood. erefore, we compared responses of birds with diering FP phenotypes to several behavioural tests at young and adult ages. We used birds from a genetic line selected for high feather pecking. FP phenotypes of individual birds were identied via FP observations at 3-4, 12-13, 15-16 and 28-29 weeks of age. e total number of severe feather pecks (SFP) given and received over two subsequent weeks was used to categorize birds as feather peckers (P, SFP given >1), feather pecker-victims (P-V, SFP given and received >1), victims (V, SFP received >1) or neutrals (N, SFP given and received 0 or 1) at each age point. Birds were tested individually in a novel environment (NE) test at 4 weeks of age, an open eld (OF) test at 15 weeks of age and a tonic immobility (TI) test at 13 and 28 weeks of age. Experimenters were blinded to the phenotypes. Data were analysed using linear mixed models, with phenotype and batch as xed factors and pen as a random factor. Test time was added as a xed eect for the NE and OF test. Experimenter was added as a xed eect for the NE and TI test. Testing order was included as a xed eect for the TI test. Phenotype eects were tested for each behavioural test and age separately using the most recent FP phenotype categorization. FP phenotype aected the number of ight attempts (F3, 119=3.18, P<0.05) during the NE test, where victims showed more ight attempts compared to neutrals (V=2.3 vs n=1.6; P<0.05) and tended to show fewer ight attempts compared to feather peckers (V=2.3 vs P=2.7; P<0.1). FP phenotype further tended to aect step frequency (F3, 75=2.64, P<0.1) during the OF test, where feather peckers tended to walk more compared to neutrals (P=24.6 vs n=15.7; P<0.1). No FP phenotype eects were found for the TI test. Feather peckers tended to show more active responses (i.e. tended to show more ight attempts compared to victims and tended to walk more compared to neutrals), which could suggest lower fearfulness, compared to victims at 4 weeks of age and compared to neutrals at 15 weeks of age. ese ndings give rst indications that FP phenotypes seem to dier in fearfulness. It should be noted that we only found dierences in the NE and OF test, where behavioural responses could also be related to activity or coping style. Further research is needed to identify whether FP phenotypes dier in activity and whether they can be classied into dierent coping styles.
Effects of (a switch in) enriched vs barren housing on the response to reward loss in pigs in a negative contrast test
Luo, Lu ; Reimert, I. ; Smeets, Sharine ; Haas, E.N. de; Parmentier, H.K. ; Kemp, B. ; Bolhuis, J.E. - \ 2018
In: Proceedings of the 52nd Congress of the International Society for Applied Ethology. - Wageningen, The Netherlands : Wageningen Academic Publishers - ISBN 9789086863228 - p. 233 - 233.
Several studies suggest that animals in a negative emotional state are more sensitive to reward losses as shown by behavioural and neurophysiological responses. In a successive negative contrast (SNC) test, reward losses are induced by decreasing the size of the reward for a task for which animals have been trained. is SNC paradigm has not been widely used in pigs. It is well known that environmental enrichment positively inuences the welfare of pigs, and may induce a more optimistic emotional state, which could reduce their sensitivity to reward losses. We studied pigs in barren (B) or enriched (E) housing, experiencing either a switch in housing conditions at 7 weeks of age or not (4 treatment groups: EE, EB, BE, BB, n=8 pens per group) in an SNC runway task. We hypothesized that B housed pigs, particularly those that changed from E to B housing, would show an enhanced sensitivity to reward losses. One pig per pen was trained to run a 24.6 m U-shaped runway for 6 pieces and one for 1 piece of apple. Each pig received 3 trials per day, with a maximum of 120 sec/trial. Latency to start eating the reward was recorded, and the average was calculated per day. Aer 11 days, all pigs received 1 piece of apple only for another 11 days (reward shi: 6-1 vs 1-1 reward group), i.e. the group originally receiving 6 pieces of apple experienced a reward loss. Eects of pre-housing, post-housing, (original) reward size, day and interactions were analysed using mixed models with a random eect of animal. Fiy-one pigs were successfully trained. Before the reward shi, over the rst 11 days, pre-housing × post-housing × reward size aected the average run-time (P<0.05). All BB pigs ran slower than other pigs (BB: 59.3±2.8; BE: 35.9±1.7; EB: 39.6±2.2; EE: 40.9±2.2, P<0.05), without any other signicant pairwise dierences. Analysis per treatment revealed, however, that EB 6-reward pigs were faster than the 1-reward pigs. Overall latency was higher on the last days (P<0.001). Aer the reward size shied to 1 on day 12, pre-housing × post-housing aected the latency (P<0.001). Post hoc analysis showed that again, BB pigs were slower than other pigs (BB: 88.2±2.7; BE 62.3±2.3; EB: 57.3±2.3; EE: 70.4±2.6, P<0.001), and EB pigs were faster than EE pigs (P<0.05). Pigs ran slower aer than before the reward shi (P<0.001). Nevertheless, pigs in the 6-1 group ran slower than pigs in the 1-1 group aer the reward shi (6-1: 73.9±2.0; 1-1: 66.4±1.8, P<0.05), suggesting that pigs are sensitive to a loss in reward size. is was, however, irrespective of housing given the lack of interactions with reward size. We conclude that housing aected the latency to run down a runway for a reward in pigs, which can indicate a lower motivation in the BB pigs, an eect that was absent in the B pigs that switched to enriched housing (BE pigs). We found, however, no evidence that housing or a switch in housing conditions aected the sensitivity to reward loss.
Trimbot2020 : An outdoor robot for automatic gardening
Strisciuglio, Nicola ; Tylecek, Radim ; Blaich, Michael ; Petkov, Nicolai ; Biber, Peter ; Hemming, Jochen ; Henten, Eldert van; Sattler, Torsten ; Pollefeys, Marc ; Gevers, Theo ; Brox, Thomas ; Fisher, Robert B. - \ 2018
In: 50th International Symposium on Robotics, ISR 2018. - - 1 p.

Robots are increasingly present in modern industry and also in everyday life. Their applications range from health-related situations, for assistance to elderly people or in surgical operations, to automatic and driver-less vehicles (on wheels or flying) or for driving assistance. Recently, an interest towards robotics applied in agriculture and gardening has arisen, with applications to automatic seeding and cropping or to plant disease control, etc. Autonomous lawn mowers are succesful market applications of gardening robotics. In this paper, we present a novel robot that is developed within the TrimBot2020 project, funded by the EU H2020 program. The project aims at prototyping the first outdoor robot for automatic bush trimming and rose pruning.

Operational, environmental, and resource productivity factors driving spatial distribution of gillnet and longline fishers targeting Nile-perch (Lates niloticus), Lake Victoria
Peter, Happy K. ; Zwieten, Paul A.M. van - \ 2018
Journal of Great Lakes Research 44 (2018)6. - ISSN 0380-1330 - p. 1235 - 1251.
Effort allocation - Encounter rate - Ideal free distribution - Patch density - Resource space - Size-productivity spectrum

Operational and environmental factors limited available resource space of gillnet and longline fishers targeting Nile perch in the Speke gulf and open lake of southern Lake Victoria and drove their encounter rates with patches of fish resulting in gear specific distributional patterns. Catch-rate patterns were similar by region and gear: large (>50 cm) Nile-perch densities increased over distance from homeport and deeper in the water column while small Nile perch (<50 cm) densities decreased. Effects of season, (setting) depth and region were present but small and obscured by high variation in daily catch-rates and individual fisher strategies. Both fisheries distributed themselves over the size-productivity spectrum of Nile perch but reacted differently to patterns in size distribution of Nile perch: gillnetters focused more on numbers of productive juveniles between 30 and 60 cm at on average 5 km distance (59 min travel time) from homeport and longliners on larger sized 40–80 cm Nile perch deeper in the water column at 7 km (108 min). Sampled fishers likely were representative of most of the Nile perch fisheries. If so, this means that fishing pressure is mainly exerted on nearshore lake areas, and more lightly fished offshore areas may act as a refuge for adult Nile perch. Total catch-rates by gear were generally equalized over the resource space, increasing slightly with distance from homeport, according to ideal free distribution predictions. Nile perch fishers on Lake Victoria appear to distribute themselves according to the underlying productivity distribution of the resource within the constraints of their available resource space.

Fisher responses to private monitoring interventions in an Indonesian tuna handline fishery
Doddema, Mandy ; Spaargaren, Gert ; Wiryawan, Budy ; Bush, Simon R. - \ 2018
Fisheries Research 208 (2018). - ISSN 0165-7836 - p. 49 - 57.
Fisher behavior - Fishery-dependent data collection - Information technology - Small-scale fisheries - tuna

Information is central to the assessment and regulation of fisheries, yet underreporting remains a persistent problem, especially in the small-scale and developing country fisheries. Private actors, using a variety of enumeration approaches and technologies, have started to supplement government enumeration programs to meet a range of reporting obligations. This paper introduces a social practices approach to understand the response of fishers to private enumeration interventions. We base our analysis on the introduction of landing enumeration, fisher logbooks and Spot Trace devices by the Indonesian NGO, Masyarakat dan Perikanan Indonesia (MDPI) in a Fair Trade USA certified handline tuna fishery in Eastern Indonesia. The results show how a social practices approach offers a grounded understanding of responses to monitoring interventions that extends beyond conventional analyses of fishery-dependent data collection. The paper concludes that understanding data collection as a set of socially mediated practices that intervene in established fishing and landing practices can help to improve the design of fisheries data collection.

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

Geostatistical disaggregation of polygon maps of average crop yields by area-to-point kriging
Brus, D.J. ; Boogaard, H. ; Ceccarelli, T. ; Orton, T.G. ; Traore, S. ; Zhang, M. - \ 2018
European Journal of Agronomy 97 (2018). - ISSN 1161-0301 - p. 48 - 59.
Aggregated data - Uncertainty - Yield gap

Crop yield data are often available as statistics of areas, such as administrative units, generated by national agricultural surveys and censuses. This paper shows that such areal data can be used in area-to-point kriging (ATP kriging) to estimate the crop yield at the nodes of a fine grid that discretizes the study area, so that a more detailed map of the crop yield is obtained. The theory behind ATP kriging is explained, and illustrated with a one-dimensional simulation study and two real-world case studies. Vegetation, precipitation, temperature and soil data were used as potential covariates in the spatial trend part of the geostatistical model. ATP kriging requires the covariogram at point support, which can be recovered from the areal data by restricted maximum likelihood. The standard errors of the estimated variogram parameters can then be obtained by the Fisher information matrix. The average yields of only 17 administrative units in Shandong province (China) were not enough to obtain reliable estimates of the covariogram at point support. Also the ranges of the regional averages of the covariates were very narrow, so that the model must be extrapolated in the largest part of the study area. We were more confident about the covariogram parameters estimated from 45 provinces in Burkina Faso. We conclude that ATP kriging is an interesting method for disaggregation of spatially averaged crop yields. Contrary to other downscaling methods ATP kriging is founded on statistical theory, and consequently provides estimates of the precision of the disaggregated yields. Shortcomings are related to the uncertainty in the estimated covariogram parameters, as well as to the extrapolation of the model outside the range of the regional means of the covariates. Opportunities for future advancements are the use of modelled yields as covariates and the introduction of expert knowledge at different levels. For the latter a Bayesian approach to ATP kriging can be advantageous, introducing prior knowledge about the model parameters, as well as accounting for uncertainty about the model parameters.

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