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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    Gene interactions observed with the HDL-c blood lipid, intakes of protein, sugar and biotin in relation to circulating homocysteine concentrations in a group of black South Africans
    Plessis, Jacomina P. du; Melse-Boonstra, Alida ; Zandberg, Lizelle ; Nienaber-Rousseau, Cornelie - \ 2020
    Molecular Genetics and Metabolism Reports 22 (2020). - ISSN 2214-4269
    Biotin - Blood lipid–gene interactions - Gene–diet interactions - Hyperhomocysteinemia - Nutrient–gene interactions - Nutrigenetics - Precision nutrition - Protein - Sugar - Total homocysteine

    Background: Elevated homocysteine (Hcy) is associated with several pathologies. Gene–diet interactions related to Hcy might be used to customize dietary advice to reduce disease incidence. To explore this possibility, we investigated interactions between anthropometry, biochemical markers and diet and single-nucleotide polymorphisms (SNPs) in relation to Hcy concentrations. Five SNPs of Hcy-metabolizing enzymes were analyzed in 2010 black South Africans. Results: Hcy was higher with each additional methylenetetrahydrofolate reductase (MTHFR) C677T minor allele copy, but was lower in methionine synthase (MTR) 2756AA homozygotes than heterozygotes. Individuals harboring cystathionine β synthase (CBS) 833 T/844ins68 had lower Hcy concentrations than others. No interactive effects were observed with any of the anthropometrical markers. MTHFR C677T and CBS T833C/844ins68 homozygote minor allele carriers presented with lower Hcy as high density lipoprotein cholesterol (HDL-c) increased. Hcy concentrations were negatively associated with dietary protein and animal protein intake in the TT and TC genotypes, but positively in the CC genotype of CBS T833C/844ins68. Hcy was markedly higher in TT homozygotes of MTHFR C677T as added sugar intake increased. In CBS T833C/844ins68 major allele carriers, biotin intake was negatively associated with Hcy; but positively in those harboring the homozygous minor allele. Conclusions: The Hcy–SNP associations are modulated by diet and open up the possibility of invoking dietary interventions to treat hyperhomocysteinemia. Future intervention trials should further explore the observed gene–diet and gene–blood lipid interactions.

    Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
    Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
    Domestication - Evolution - Gene flow - Neolithic

    Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

    Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
    Lees, John A. ; Ferwerda, Bart ; Kremer, Philip H.C. ; Wheeler, Nicole E. ; Valls Serón, Mercedes ; Croucher, Nicholas J. ; Gladstone, Rebecca A. ; Bootsma, Hester J. ; Rots, Nynke Y. ; Wijmega-Monsuur, Alienke J. ; Sanders, Elisabeth A.M. ; Trzciński, Krzysztof ; Wyllie, Anne L. ; Zwinderman, Aeilko H. ; Berg, Leonard H. van den; Rheenen, Wouter van; Veldink, Jan H. ; Harboe, Zitta B. ; Lundbo, Lene F. ; Groot, Lisette C.P.G.M. de; Schoor, Natasja M. van; Velde, Nathalie van der; Ängquist, Lars H. ; Sørensen, Thorkild I.A. ; Nohr, Ellen A. ; Mentzer, Alexander J. ; Mills, Tara C. ; Knight, Julian C. ; Plessis, Mignon du; Nzenze, Susan ; Weiser, Jeffrey N. ; Parkhill, Julian ; Madhi, Shabir ; Benfield, Thomas ; Gottberg, Anne von; Ende, Arie van der; Brouwer, Matthijs C. ; Barrett, Jeffrey C. ; Bentley, Stephen D. ; Beek, Diederik van de - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723 - 14 p.

    Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.

    Spatial separation of semiochemical Lurem-TR and entomopathogenic fungi to enhance their compatibility and infectivity in an autoinoculation system for thrips management
    Mfuti, D.K. ; Subramanian, S. ; Tol, R.W.H.M. van; Wiegers, G.L. ; Kogel, W.J. de; Niassy, S. ; Plessis, H. du; Ekesi, S. ; Maniania, N.K. - \ 2016
    Pest Management Science 72 (2016)1. - ISSN 1526-498X - p. 131 - 139.

    The effect of spatial separation of the semiochemical Lurem-TR, which has been found to inhibit conidia of entomopathogenic fungi when put together, on the persistence of conidia of Metarhizium brunneum and M. anisopliae was evaluated in the greenhouse and field in order to develop an autodissemination strategy for the management of Megalurothrips sjostedti on cowpea crop. Influence of spatial separation of the semiochemical on thrips attraction and conidial acquisition by thrips from the autoinoculation device was also investigated in the field.
    Persistence of conidia of M. brunneum and M. anisopliae increased with distance of separation of Lurem-TR. Direct exposure of fungus without separation from Lurem-TR recorded the lowest conidial germination as compared with the other treatments. Attraction of thrips to the device also varied significantly according to distance between device and semiochemical, with a higher number of thrips attracted when Lurem-TR was placed in a container below the device and at 10 cm distance. There was no significant difference in conidial acquisition between spatial separation treatments of conidia and Lurem-TR. Attraction of other insect pests to the device did not significantly vary between treatments. Positive correlations were found between conidial acquisition and thrips attraction.
    This study suggests that spatial separation of fungal conidia from Lurem-TR in an autoinoculation device could provide a low-cost strategy for effective management of thrips in grain legume cropping systems.

    Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
    Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
    Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
    abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms

    The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.

    klimaatsverandering gee dalk meer aartappels (interview met Anton Haverkort en Linus Franke)
    Botha, L. ; Franke, A.C. ; Plessis, M. ; Haverkort, A.J. ; Agrosysteemkunde, ; Plant Production Systems (PPS), - \ 2012
    Landbouweekblad 2012 (2012)1739. - ISSN 0023-7779 - p. 36 - 37.
    Integrating remote sensing and ancillary data for regional ecosystem assessment: Eucalyptus grandis agro-system in Kwazulu-Natal, South Africa
    Cho, M.A. ; Aardt, J. van; Main, R. ; Majeke, B. ; Ramoelo, A. ; Mathieu, R. ; Norris-Rogers, M. ; Plessis, M. Du - \ 2009
    In: International Geoscience and Remote Sensing Symposium (IGARSS), Cape Town, South Africa, 12 - 17 July, 2009. - Institute of Electrical and Electronics Engineers - ISBN 9781424433957 - p. IV264 - IV267.
    The ability of various ecosystems to perform vital functions such as biodiversity production, and water, energy and nutrient cycling depends on the ecosystem state, i.e. health. Ecosystem state assessment has been a topic of intense research, but has reached a point at which accurate large scale (e.g. regional to global scale) modelling and monitoring are hindered by limitations in conventional assessment methods such as direct field sampling, modelling from environmental drivers such as temperature, precipitation and available nutrients, and modelling from remote sensing data. The Ecosystem-Earth Observation (Eco-EO) research group at the Council for Scientific and Industrial Research (CSIR), South Africa has highlighted the need in remote sensing research for an integrated sensing approach at the systems level. This perspective is based on the assumption that a modelling approach that exploits the strength of the various techniques (in situ environmental variables, direct field observation and remote sensing data) could potentially improve the assessment of ecosystem state at various geographic scales. In this light, the Eco-EO research group has embarked on an agro-system state assessment project since 2007 as a first step towards the implementation of the integrated modelling approach for various ecosystems. The agro-system consists of a monoculture forest plantation of Eucalyptus grandis situated in KwaZulu-Natal, South Africa. This paper presents preliminary results from the KwaZulu-Natal E. grandis experimental study. ©2009 IEEE.
    Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini
    Greyling, B.J. ; Kryger, P. ; Plessis, S. du; Hooft, W.F. van; Helden, P. van; Getz, W.M. ; Bastos, A.D.S. - \ 2008
    African journal of biotechnology 7 (2008)5. - ISSN 1684-5315 - p. 655 - 660.
    syncerus caffer - polymorphic bovine - southern africa - linkage map - buffalo - markers - identification - cattle
    Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was established for this purpose. Mean allelic richness per locus was 8.24 and 6.47, for buffalo and Bonsmara cattle, respectively, whilst an unbiased match probability of 6.5x×10-17 and 1.03 × 10-16 was obtained for each. These results confirm the usefulness of this rapid, cost-effective typing approach for forensic, paternity and fine-scale genetic analyses of wild and domestic African Bovini tribe members
    A comparison of plant form and browsing height selection of four small stock breeds - Preliminary results
    Plessis, I. ; Waal, C. van der; Webb, E.C. - \ 2004
    South African Journal of Animal Science = Suid-Afrikaanse Tydskrif Vir Veekun 34 (2004)Suppl. 1. - ISSN 0375-1589 - p. 31 - 34.
    A direct observation technique was used to establish the foraging behaviour of Boer goats, Nguni goats, Pedi sheep and Dorper sheep. According to the Chi-square dissimilarity measure, plant-form (grass, forb, woody) differences between the diets of goats and sheep were greater than differences between the goat breeds and sheep breeds. The results from this study confirm that goats and sheep exhibit different foraging strategies. Sheep tend to forage more frequently from the herbaceous layer compared to goats, which also browse substantially from woody plants. Both goats and sheep increase their relative intake of woody plant products in winter. Goats tend to increase their woody browsing height in winter, probably adapting their foraging behaviour to fit differences in the canopy structures of prominent summer and winter forage species. Further research should be conducted to determine whether subtle differences in the foraging habits of different goat and sheep breeds exist.
    Upscaling from pore to core : effects of strong capillary forces and wettability phenomena
    Hoffmann, M.R. ; Plessis, J.P. du - \ 2000
    In: 7th European Conference on the Mathematics of Oil Recovery : , Baveno, Italy, 5-8 September 2000 Houten, The Netherlands : EAGE Business Office - p. 68 - 74.
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