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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The mechanisms underlying seasonal timing of breeding : a multi-level approach using bi-directional genomic selection on timing of egg-laying
Verhagen, Irene Charlotte - \ 2019
Wageningen University. Promotor(en): M.E. Visser, co-promotor(en): V.N. Laine. - Wageningen : Wageningen University - ISBN 9789463950398 - 221
Impact of food odors signaling specific taste qualities and macronutrient content on saliva secretion and composition
Morquecho-Campos, Paulina ; Bikker, Floris J. ; Nazmi, Kamran ; Graaf, Kees de; Laine, Marja L. ; Boesveldt, S. - \ 2019
Appetite 143 (2019). - ISSN 0195-6663
Cephalic phase response - Olfaction - Salivary protein - Salivation - Smell

Olfactory food cues can induce appetite for similar food products in humans. Odors may thus signal essential information about a foods’ composition such as taste or even macronutrient content and may stimulate specific physiological responses in anticipation of food intake. Several studies have shown that sensory food cues could stimulate saliva secretion. However, potential differences between food odors in their effect on saliva secretion, or the effects of olfactory stimulation on changes in saliva composition remain to be elucidated. To gain more insight, we conducted two studies to determine the influence of various odors, representing different taste qualities (study 1) and macronutrients (study 2), on salivary biomarkers. In study 1, 36 participants were randomly exposed to no-odor, non-food, and odors signaling sweet, savory, and sour taste. In study 2, 60 participants were randomly exposed to no-odor, non-food, and odors signaling carbohydrates, protein, fat, and low-calorie food. For each condition, whole-mouth saliva was collected and saliva secretion rate determined. Furthermore, we determined mouth-watering perception (subjective salivation), visco-elasticity (study 1 only), mucin concentration, α-amylase and lingual lipase activity (study 2 only). For both studies, linear mixed model analyses showed that saliva secretion rate significantly increased by food odor exposure compared to no-odor and non-food conditions. However, no changes in salivary composition were observed. These findings indicate that food odors play a crucial role in anticipatory saliva responses and can thereby affect subsequent eating behavior.

The Genomic Complexity of a Large Inversion in Great Tits
Silva, Vinicius H. da; Laine, Veronika N. ; Bosse, Mirte ; Spurgin, Lewis G. ; Derks, Martijn F.L. ; Oers, Kees van; Dibbits, Bert ; Slate, Jon ; Crooijmans, Richard P.M.A. ; Visser, Marcel E. ; Groenen, Martien A.M. - \ 2019
Genome Biology and Evolution 11 (2019)7. - ISSN 1759-6653 - p. 1870 - 1881.
Parus major - CNVs - songbird - structural variation

Chromosome inversions have clear effects on genome evolution and have been associated with speciation, adaptation, and the evolution of the sex chromosomes. In birds, these inversions may play an important role in hybridization of species and disassortative mating. We identified a large (≈64 Mb) inversion polymorphism in the great tit (Parus major) that encompasses almost 1,000 genes and more than 90% of Chromosome 1A. The inversion occurs at a low frequency in a set of over 2,300 genotyped great tits in the Netherlands with only 5% of the birds being heterozygous for the inversion. In an additional analysis of 29 resequenced birds from across Europe, we found two heterozygotes. The likely inversion breakpoints show considerable genomic complexity, including multiple copy number variable segments. We identified different haplotypes for the inversion, which differ in the degree of recombination in the center of the chromosome. Overall, this remarkable genetic variant is widespread among distinct great tit populations and future studies of the inversion haplotype, including how it affects the fitness of carriers, may help to understand the mechanisms that maintain it.

Exploring the unmapped DNA and RNA reads in a songbird genome
Laine, Veronika N. ; Gossmann, Toni I. ; Oers, Kees van; Visser, Marcel E. ; Groenen, Martien A.M. - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Contamination - DNA sequencing - Pathogens - RNA sequencing - Unmapped reads

Background: A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence. Results: Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma. Conclusions: Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

Affymetrix SNP array data for wild Dutch great tits (Parus major)
Silva, Vinicius Da; Laine, Veronika N. ; Bosse, M. ; Oers, C.H.J. ; Dibbits, B.W. ; Visser, M.E. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2018
GSE105131 - Parus major - PRJNA415009
The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.
CNVs are associated with genomic architecture in a songbird
Silva, Vinicius H. da; Laine, Veronika N. ; Bosse, Mirte ; Oers, Kees van; Dibbits, Bert ; Visser, Marcel E. ; Crooijmans, Richard P.M.A. ; Groenen, Martien A.M. - \ 2018
BMC Genomics 19 (2018)Supplement 2. - ISSN 1471-2164
Duplication - Genetic variation - Inheritance - Parus major - Recombination

Background: Understanding variation in genome structure is essential to understand phenotypic differences within populations and the evolutionary history of species. A promising form of this structural variation is copy number variation (CNV). CNVs can be generated by different recombination mechanisms, such as non-allelic homologous recombination, that rely on specific characteristics of the genome architecture. These structural variants can therefore be more abundant at particular genes ultimately leading to variation in phenotypes under selection. Detailed characterization of CNVs therefore can reveal evolutionary footprints of selection and provide insight in their contribution to phenotypic variation in wild populations. Results: Here we use genotypic data from a long-term population of great tits (Parus major), a widely studied passerine bird in ecology and evolution, to detect CNVs and identify genomic features prevailing within these regions. We used allele intensities and frequencies from high-density SNP array data from 2,175 birds. We detected 41,029 CNVs concatenated into 8,008 distinct CNV regions (CNVRs). We successfully validated 93.75% of the CNVs tested by qPCR, which were sampled at different frequencies and sizes. A mother-daughter family structure allowed for the evaluation of the inheritance of a number of these CNVs. Thereby, only CNVs with 40 probes or more display segregation in accordance with Mendelian inheritance, suggesting a high rate of false negative calls for smaller CNVs. As CNVRs are a coarse-grained map of CNV loci, we also inferred the frequency of coincident CNV start and end breakpoints. We observed frequency-dependent enrichment of these breakpoints at homologous regions, CpG sites and AT-rich intervals. A gene ontology enrichment analyses showed that CNVs are enriched in genes underpinning neural, cardiac and ion transport pathways. Conclusion: Great tit CNVs are present in almost half of the genes and prominent at repetitive-homologous and regulatory regions. Although overlapping genes under selection, the high number of false negatives make neutrality or association tests on CNVs detected here difficult. Therefore, CNVs should be further addressed in the light of their false negative rate and architecture to improve the comprehension of their association with phenotypes and evolutionary history.

Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait
Bosse, M. ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, I.C. ; Groenen, M. ; Oers, C.H.J. ; Sheldon, Ben C. ; Visser, M.E. ; Slate, Jon - \ 2017
adaptation - evolution - genomics - natural selection - bill length - birds - Parus major
We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
Avian Ecological Epigenetics: the role of DNA methylation in the evolution of animal personality
Oers, K. van; Derks, M.F.L. ; Schachtschneider, K.M. ; Laine, Veronika N. ; Madsen, O. ; Verhoeven, Koen J.F. - \ 2017
Recent natural selection causes adaptive evolution of an avian polygenic trait
Bosse, Mirte ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, Irene ; Groenen, Martien A.M. ; Oers, Kees van; Sheldon, Ben C. ; Visser, Marcel E. ; Slate, Jon - \ 2017
Science 358 (2017)6361. - ISSN 0036-8075 - p. 365 - 368.

We used extensive data froma long-term study of great tits (Parusmajor) in theUnitedKingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes.We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirmthat these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.

Global methane emission estimates for 2000-2012 from CarbonTracker Europe-CH4 v1.0
Tsuruta, Aki ; Aalto, Tuula ; Backman, Leif ; Hakkarainen, Janne ; Laan-Luijkx, Ingrid T. Van Der; Krol, Maarten C. ; Spahni, Renato ; Houweling, Sander ; Laine, Marko ; Dlugokencky, Ed ; Gomez-Pelaez, Angel J. ; Schoot, Marcel Van Der; Langenfelds, Ray ; Ellul, Raymond ; Arduini, Jgor ; Apadula, Francesco ; Gerbig, Christoph ; Feist, D.G. ; Kivi, Rigel ; Yoshida, Yukio ; Peters, Wouter - \ 2017
Geoscientific Model Development 10 (2017)3. - ISSN 1991-959X - p. 1261 - 1289.

We present a global distribution of surface methane (CH4) emission estimates for 2000-2012 derived using the CarbonTracker Europe-CH4 (CTE-CH4) data assimilation system. In CTE-CH4, anthropogenic and biospheric CH4 emissions are simultaneously estimated based on constraints of global atmospheric in situ CH4 observations. The system was configured to either estimate only anthropogenic or biospheric sources per region, or to estimate both categories simultaneously. The latter increased the number of optimizable parameters from 62 to 78. In addition, the differences between two numerical schemes available to perform turbulent vertical mixing in the atmospheric transport model TM5 were examined. Together, the system configurations encompass important axes of uncertainty in inversions and allow us to examine the robustness of the flux estimates. The posterior emission estimates are further evaluated by comparing simulated atmospheric CH4 to surface in situ observations, vertical profiles of CH4 made by aircraft, remotely sensed dry-air total column-averaged mole fraction (XCH4) from the Total Carbon Column Observing Network (TCCON), and XCH4 from the Greenhouse gases Observing Satellite (GOSAT). The evaluation with non-assimilated observations shows that posterior XCH4 is better matched with the retrievals when the vertical mixing scheme with faster interhemispheric exchange is used. Estimated posterior mean total global emissions during 2000-2012 are 516 ± 51 Tg CH4 yr-1, with an increase of 18 Tg CH4 yr-1 from 2000-2006 to 2007-2012. The increase is mainly driven by an increase in emissions from South American temperate, Asian temperate and Asian tropical TransCom regions. In addition, the increase is hardly sensitive to different model configurations ( < 2 Tg CH4 yr-1 difference), and much smaller than suggested by EDGAR v4.2 FT2010 inventory (33 Tg CH4 yr-1), which was used for prior anthropogenic emission estimates. The result is in good agreement with other published estimates from inverse modelling studies (16-20 Tg CH4 yr-1). However, this study could not conclusively separate a small trend in biospheric emissions (-5 to +6.9 Tg CH4 yr-1) from the much larger trend in anthropogenic emissions (15-27 Tg CH4 yr-1). Finally, we find that the global and North American CH4 balance could be closed over this time period without the previously suggested need to strongly increase anthropogenic CH4 emissions in the United States. With further developments, especially on the treatment of the atmospheric CH4 sink, we expect the data assimilation system presented here will be able to contribute to the ongoing interpretation of changes in this important greenhouse gas budget.

The Conserved Functional Role of Non-CpG Methylation in Mammalian and Avian Brain
Schachtschneider, K.M. ; Madsen, O. ; Laine, V.N. ; Derks, M.F.L. ; Schook, Lawrence B. ; Groenen, M. ; Verhoeven, K. ; Oers, K. van - \ 2016
Past selection and local adaptation in European great tit genomes
Bosse, M. ; Spurgin, L.G. ; Slate, J. ; Groenen, M. ; Laine, V.N. ; Oers, Kees van; Visser, M.E. - \ 2016
Lactobacillus rhamnosus GG Outcompetes Enterococcus faecium via Mucus-Binding Pili : Evidence for a Novel and Heterospecific Probiotic Mechanism
Tytgat, Hanne L.P. ; Douillard, François P. ; Reunanen, Justus ; Rasinkangas, Pia ; Hendrickx, Antoni P.A. ; Laine, Pia K. ; Paulin, Lars ; Satokari, Reetta ; Vos, Willem M. de - \ 2016
Applied and Environmental Microbiology 82 (2016)19. - ISSN 0099-2240 - p. 5756 - 5762.

Vancomycin-resistant enterococci (VRE) have become a major nosocomial threat. Enterococcus faecium is of special concern, as it can easily acquire new antibiotic resistances and is an excellent colonizer of the human intestinal tract. Several clinical studies have explored the potential use of beneficial bacteria to weed out opportunistic pathogens. Specifically, the widely studied Lactobacillus rhamnosus strain GG has been applied successfully in the context of VRE infections. Here, we provide new insight into the molecular mechanism underlying the effects of this model probiotic on VRE decolonization. Both clinical VRE isolates and L. rhamnosus GG express pili on their cell walls, which are the key modulators of their highly efficient colonization of the intestinal mucosa. We found that one of the VRE pilus clusters shares considerable sequence similarity with the SpaCBA-SrtC1 pilus cluster of L. rhamnosus GG. Remarkable immunological and functional similarities were discovered between the mucus-binding pili of L. rhamnosus GG and those of the clinical E. faecium strain E1165, which was characterized at the genome level. Moreover, E. faecium strain E1165 bound efficiently to mucus, which may be prevented by the presence of the mucus-binding SpaC protein or antibodies against L. rhamnosus GG or SpaC. These results present experimental support for a novel probiotic mechanism, in which the mucus-binding pili of L. rhamnosus GG prevent the binding of a potential pathogen to the host. Hence, we provide a molecular basis for the further exploitation of L. rhamnosus GG and its pilins for prophylaxis and treatment of VRE infections.

The copy number variations at genes related to neuronal functions under selection in great tit
Silva, Vinicius da; Laine, V.N. ; Bosse, M. ; Oers, C.H.J. ; Gienapp, P. ; Visser, M.E. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2016
The great tit (Parus major) is a well-studied wild bird which has been used as a model species to document the effects of global warming on nature. The recent completion of a reference genome sequence of the great tit and the availability of a high density (HD) 500K SNP-chip, have enabled detailed genomic studies in this species. These genomic tools allowed precise and scalable measures of genetic and non-genetic (i.e. epigenetic marks) variation as well the identification of SNP variants under selection. Here we present an initial copy number variation (CNV) analysis in great tit genomes using the HD SNP-chip intensities and allele frequencies from over 2000 females. We found regions of CNVs (CNVRs) significantly enriched for neuronal related pathways as ‘neuroactive ligant-receptor interaction’ and ‘Gap junction’. Interestingly, genes related to neuronal functions were previously identified at regions under positive selection and prone to be methylated in great tits. This suggests that complex variation (CNV + SNP + methylation) plays an important role in great tit microevolution. A representative example is the gene CD200 which is associated with Parkinson´s disease, neuroimmunity, and is under positive selection in the Dutch great tit population and overlaps a highly frequent CNVR. The CNV analysis is at an early stage and the next steps include strategies to improve the SNP-chip overall signal quality, SNP-CNV haplotype reconstruction, a selection analysis as well as a genome-wide association study for seasonal phenotypes (e.g. timing of breeding) changing as a result of global warming.
The copy number variations at genes related to neuronal functions under selection in great tit
Silva, Vinicius da; Groenen, M. ; Bosse, M. ; Crooijmans, R.P.M.A. ; Laine, V.N. ; Oers, K. van; Gienapp, P. ; Visser, M.E. - \ 2016
Complete Genome Sequence of Enterococcus faecium Commensal Isolate E1002
Tytgat, Hanne ; Douillard, F.P. ; Laine, P.K. ; Paulin, L. ; Willems, R.J.L. ; Vos, W.M. de - \ 2016
Genome Announcements 4 (2016)2. - ISSN 2169-8287
The emergence of vancomycin-resistant enterococci (VRE) has been associated with an increase in multidrug-resistant nosocomial infections. Here, we report the 2.614-Mb genome sequence of the Enterococcus faecium commensal isolate E1002, which will be instrumental in further understanding the determinants of the commensal and pathogenic lifestyle of E. faecium.
Evolutionary signals of selection on cognition from the great tit genome and methylome
Laine, V.N. ; Gossmann, T.I. ; Schachtschneider, K.M. ; Garroway, C.J. ; Madsen, Ole ; Verhoeven, K.J.F. ; Jager, Victor De; Megens, Hendrik Jan ; Warren, W.C. ; Minx, Patrick ; Crooijmans, R.P.M.A. ; Corcoran, Pádraic ; Adriaensen, Frank ; Belda, Eduardo ; Bushuev, Andrey ; Cichon, Mariusz ; Charmantier, Anne ; Dingemanse, Niels ; Doligez, Blandine ; Eeva, Tapio ; Erikstad, Kjell Einar ; Fedorov, Slava ; Hau, Michaela ; Hille, Sabine ; Hinde, Camilla ; Kempenaers, Bart ; Kerimov, Anvar ; Krist, Milos ; Mand, Raivo ; Matthysen, Erik ; Nager, Reudi ; Norte, Claudia ; Orell, Markku ; Richner, Heinz ; Slagsvold, Tore ; Tilgar, Vallo ; Tinbergen, Joost ; Torok, Janos ; Tschirren, Barbara ; Yuta, Tera ; Sheldon, B.C. ; Slate, Jon ; Zeng, Kai ; Oers, Kees Van; Visser, M.E. ; Groenen, M.A.M. - \ 2016
Nature Communications 7 (2016). - ISSN 2041-1723

For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

Assessing resilience of dairy cattle by studying impact of heat stress on predicted feed intake
Vanrobays, M.L. ; Hammami, Hedi ; laine, Aurelie ; Soyeurt, Hélène ; Vandenplas, J. ; Froidmont, E. ; Gengler, Nicolas - \ 2015
In: Feeding behaviour as an indicator of health and welfare. - DairyCare COST Action FA1308 - ISBN 9780993017629 - p. 49 - 49.
Milk production and feed intake of dairy cows are both affected by heat stress (HS) which is also a potentially important cause of discomfort for animals. Therefore, strategies allowing mitigation of HS effects are required. Genetic selection appears to be a good solution because this tool permits to improve cumulatively and continuously traits of interest. In this context, the goal of this study was to estimate genetic variation of milk yield and predicted feed intake over the whole trajectory of temperature humidity index (THI) using a reaction norm approach. A total of 30,161 fat and protein corrected milk (FPCM) yield records from 4,577 Holstein cows were used. These data were collected between June 2009 and December 2010 in 453 herds in the Walloon Region of Belgium. Daily dry matter intake (DMI; g/d) of dairy cows were estimated at the day of FPCM records from the prediction equation of NRC (2001), which is based on predicted body weight, FPCM, and week of lactation. Body weight of cows was estimated using a two-step approach allowing to predict body weight throughout the lactation from body weight calculated using linear conformation traits. Daily values of THI were computed from meteorological data using the mean of daily values of dry bulb temperature and relative humidity. Bivariate random regression test-day models with random linear regressions on THI values were developed for FPCM and DMI. Estimated average daily heritability for FCPM was 0.08 and decreased slightly at extreme THI values (from 0.10 (THI = 17) to 0.06 (THI =75)). Heritabilities of DMI also decreased with increasing THI values: from 0.11 (THI=17) to 0.05 (THI=75). Genetic correlations between FPCM and DMI were positive and ranged from 0.85 (THI=17) to 0.55 (THI=75). This decrease could be explained by the decrease of DMI under HS which could be balanced by the buffering effect of body tissue mobilization. Combining these novel results with known effects of HS on body fat mobilization might help to disentangle complex relationships between mobilization and intake under HS; this being also an important issue in assessing well-being of dairy cattle and their resilience potential to HS.
Finding the genes which make great tits innovators
Laine, V. ; Gossmann, T.I. ; Schachtschneider, K.M. ; Madsen, O. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Oers, K. van; Visser, M.E. ; Groenen, M. - \ 2015
The genomics of avian breeding time – an ecologically relevant trait for adaptation to climate change
Gienapp, P. ; Calus, M.P.L. ; Laine, V. ; Oers, K. van; Groenen, M. ; Slate, J. ; Visser, M.E. - \ 2015
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