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

Dairy cow preference for access to an outdoor pack in summer and winter
Smid, A.M.C. ; Burgers, E.E.A. ; Weary, D.M. ; Bokkers, E.A.M. ; Keyserlingk, M.A.G. von - \ 2019
Journal of Dairy Science 102 (2019)2. - ISSN 0022-0302 - p. 1551 - 1558.
alternative housing - animal welfare - exercise lot - outdoor area

The aim of our study was to test the preference of freestall-housed dairy cows to access an outdoor deep-bedded open pack (versus remaining inside the freestall barn) in the summer and winter. A secondary aim was to investigate how preference for outdoor access influenced feeding, lying, and stall perching behavior. Eight groups of pregnant, lactating cows were tested in the summer and 9 groups in the winter. During both experiments, groups were allowed to stabilize for 5 d, followed by 2 d of baseline observations (baseline phase). Habituation to the outdoor pack took place for the next 2 d. Cows were then provided free access to the outdoor pack continuously for 5 d (choice phase). During the choice phase, in addition to feeding and perching behavior (recorded while cows were inside the barn), cow location (i.e., in the freestall pen or on the outdoor pack) was also noted. We used HOBO data loggers (Onset Computer Corp., Bourne, MA) to automatically record lying behavior during baseline and choice phases. Cows spent a mean ± standard error (minimum to maximum in parentheses) of 25.3 ± 4.3% (8.0 to 44.5%) of the time outside in the summer and 1.8 ± 0.6% (0.1 to 4.1%) in the winter. In the summer, cows spent more time on the outdoor pack during night (50.0 ± 8.4% between 2000 and 0600 h) than during the day (3.3 ± 1.3% between 0600 and 2000 h). In the winter, we found no effect of time of day on time spent outside (day = 1.7 ± 0.7%; night = 2.1 ± 1.0%). Precipitation decreased the time cows spent outside during summer nights. During winter days, precipitation and increasing wind speeds decreased the time cows spent outside. In the summer, time spent feeding was higher during the baseline phase (18.7 ± 0.3%) than during the choice phase (17.4 ± 0.3%). During the winter, no difference in feeding time was found between the 2 phases (baseline = 18.7 ± 0.3%; choice = 18.4 ± 0.3%). During the summer, cows spent more time perching during the baseline phase (6.5 ± 0.5%) than during the choice phase (3.6 ± 0.5%) and this tended to be true during the winter (baseline = 5.5 ± 0.7%; choice = 4.5 ± 0.7%). Daily lying time did not differ between the baseline and choice phases in either the summer (baseline = 59.6 ± 0.9%; choice = 57.7 ± 0.9%) or winter (baseline = 63.0 ± 1.2%; choice = 62.6 ± 1.2%). When on the outdoor pack, cows spent 53.7% (±5.6) of the time lying during the summer and 4.7% (±2.5) during the winter. In conclusion, during the summer cows displayed a partial preference to be outside on a deep-bedded open pack when given the opportunity, especially during the night, but in the winter cows spent little time on the outdoor pack.

The FAIR Guiding Principles for scientific data management and stewardship : Comment
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2016
Scientific Data 3 (2016). - ISSN 2052-4463

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Toward effective software solutions for big biology (Letter to the Editor)
Prins, J.C.P. ; Ligt, J. de; Tarasov, A. ; Jansen, R.C. ; Cuppen, E. ; Bourne, P.E. - \ 2015
Nature Biotechnology 33 (2015). - ISSN 1087-0156 - p. 686 - 687.
Plant composition modulates arthropod pest and predatorabundance: Evidence for culling exotics and planting natives
Parry, H.R. ; Macfadyen, S. ; Hopkinson, J.E. ; Bianchi, F.J.J.A. ; Zalucki, M.P. ; Bourne, A. ; Schellhorn, N.A. - \ 2015
Basic and Applied Ecology 16 (2015)6. - ISSN 1439-1791 - p. 531 - 543.
We investigate the role of plant species in crops, pasture and native vegetation remnants in supporting agronomic pests and their predators. The study was conducted in three Australian States and across 290 sites sampled monthly for two years. Pastures played a key role in harbouring pest species consistent across States, while native vegetation hosted relatively more predators than other habitat types within each State. Furthermore, native plant species supported the lowest pest density and more predators than pests; in contrast, 75% of the exotic weed species surveyed hosted more pests than predators. Despite the role of pasture in harbouring pests, we found in NSW that pasture also supported the highest proportion of juvenile predators, while native vegetation remnants had the lowest. Our results indicate that non-crop habitat (native remnants or pasture) with few exotic weeds supports high predator and low pest arthropod densities, and that weeds are associated with high pest densities. By linking broad response variables such as ‘all pests’ with specific predictors such as ‘plant species’, our study will inform on-farm management actions of which weeds to control and which natives to plant or regenerate. This study shows the importance of knowing the function of habitats and plants species in supporting pests and predators in agricultural landscapes across multiple regions.
On the biology and evolution of fungi from soda soils
Grum-Grzhimaylo, A. - \ 2015
Wageningen University. Promotor(en): Bas Zwaan, co-promotor(en): Fons Debets. - Wageningen : Wageningen University - ISBN 9789462574281 - 232
bodemschimmels - zoute gronden - diversiteit - bodembiologie - evolutie - soil fungi - saline soils - diversity - soil biology - evolution

Summary to the thesis “On the biology and evolution of fungi from soda soils”

Alexey Grum-Grzhimaylo

The presented thesis addresses aspects of biology and evolution of fungi that were recovered from saline soda soils. The work highlights the fact that saline soda soils are populated by a large diversity of fungi capable of withstanding high salts content and high pH. Some of these fungi have been shown to require exceptionally high pH and salts to grow optimally and therefore are called alkaliphiles.

Introductory CHAPTER 1 provides examples of seemingly inhabitable environments and some of its most prominent tenants, with the emphasis on soda lakes ecosystem and alkaliphilic organisms. Aspects of physiology and major adaptive strategies to high pH and salts found in bacteria are portrayed. To our knowledge, there are no studies devoted to the fungi inhabiting saline soda lakes making this work a starting point towards further explorations in the field.

In CHAPTER 2, I show that fungi are actually present in saline soils and focus closely on the fungus that dominated across all our soda soils samples. This fungus displayed a rare obligate alkaliphilic phenotype – it was capable of growing at pH 11.4 on agar plates, with the optimum of around 9–10 and no ability to grow at pH 5.2. Using a combination of morphological and phylogenetic approaches, I describe it as a new name Sodiomyces alkalinus (previously known as Heleococcum alkalinum). We looked at the morphological details of its life cycle and tested for the capacity of utilizing various carbon sources. Given its unique extreme physiology, dominance across the soil samples, and partly for historical reasons, S. alkalinus has become our model organism that found considerable attention across this thesis.

Inspired by the fact that saline soda soils harbour new fungi, I moved on to the investigation of another set of isolates we obtained from soda soils, which belong to the Emericellopsis group (Hypocreales). CHAPTER 3 presents an investigation of the Emericellopsis isolates that showed a much broader pH preference tagging them as facultative alkaliphiles. Here again, combined morphological, phylogenetic, and physiological data allowed us to set this group apart from the rest and described it as a new species – Emericellopsis alkalina. This species is genetically unrelated to S. alkalinus, which provides evidence for the alkaliphilic trait to be polyphyletic, i.e. arisen several times throughout evolutionary history. I showed E. alkalina to be genetically closer to marine-bourne isolates than typical terrestrial species. Such a result provides evidence for the origin of alkaliphilic trait in this group from the marine-bourne fungi, as sea and soda soils environmental factors coincide.

CHAPTER 4 is devoted to a systematic study of our whole collection of fungi recovered from saline soda soils across the world. I investigate over a hundred isolates morphologically, phylogenetically, and test them for growth pH preference. These data confirms the notion that alkaliphily is polyphyletic and has emerged in several lineages of the fungal phylogenetic tree. Detailed morphological descriptions and phylogenetic reconstructions gave me confidence in describing several more new species. A prominent finding is the discovery of two additional Sodiomyces species that also show the obligate alkaliphilic adaptation. Systematic approaches let me to link certain morphological characters of the species to the alkaliphilic phenotype they possess. Although a substantial part of fungi from soda soils indeed displayed alkaliphilic capabilities, we detected typical neutrophilic species that presumably are transient or reside in a dormant state as spores or survival structures.

The next chapters of the thesis are focused on S. alkalinus, chosen as a model organism for studying alkaliphily that we sequenced in collaboration with Joint Genome Institute (Walnut Creek, USA). CHAPTER 5 looks into the aspects of the hydrolytic capabilities of S. alkalinus. The genome and transcriptome provide immense body of data that gave insight on the enzyme sets encoded in the genome involved in the degradation of carbohydrate compounds (so-called CAZymes). Such in silico analysis was backed-up by the enzyme bioassays carried out at various pH and substrates. In S. alkalinus, I found cellulolytic and hemicellulolytic enzymes that act at high pH, as opposed to neutrophilic A. oryzae enzymes that were active mostly at pH 6. Another prominent finding was the detection of strong proteolytic enzymes acting optimally at pH 8. Based on the genome data and bioassays patterns, I speculate on the ecological role of S. alkalinus in soda soils.

CHAPTER 6 addresses the aspects of the PacC transcription factor, a key player in mediating the gene expression under different ambient pH. I sought to find differences in the primary structure of PacC or detecting the multicopiness of the pacC gene, given its function under extreme alkaline conditions. It turned out that the primary structure of the PacC was the same as in other fungi and the pacC gene is presented in a single copy in S. alkalinus genome. However, I noted a shifted expression and proteolytic activation pattern of PacC if compared to neutrophilic fungi. This results provides evidence for the re-tuned pH-sensors on the plasma membrane, however we could not convincingly detect signs of positive selection affecting the PalH sensors that would change its threshold to trigger the downstream molecular cascade.

CHAPTER 7 gives insights into a quite unexpected finding – the presence of viruses in several of the S. alkalinus isolates. I show their effective vertical but not horizontal transmission. Possession of dsRNA as genetic material, icosahedral shapes, and symptomless phenotypes are common characters for a mycovirus. The virus I studied in S. alkalinus exhibits these exact same features. Curiously, no other alkaliphiles from our collection nor known sister species harboured mycoviruses, making this the first instance of mycoviruses detected in an alkaliphilic filamentous fungus.

CHAPTER 8 focuses on another peculiar finding – a bacterial gene in the genome of S. alkalinus. Presumably introduced by a horizontal gene transfer event, this gene encodes for a DD-peptidase homologue commonly found in bacteria, but only in very few eukaryotes. I found only three fungi that possess this gene; two are alkaliphilic – S. alkalinus and its sister species Acremonium alcalophilum. This suggests the importance of this gene for alkaliphily in those species. The DD-peptidase gene appears to be functional and its peak expression was observed at pH 8. Comparative analysis showed this fungal DD-peptidase to be closely related to the homologues derived from halophilic and alkaliphilic bacteria, rather than from neutrophilic ones. I speculate on the putative function of this unusual gene, including the role in the build-up of exo-cellular matrix or defense against dense communities of prokaryotes in soda soils.

The discussion in CHAPTER 9 contemplates on the results obtained throughout the thesis and provides future perspectives on the topic.

A new species of Colostethus (Anura, Dendrobatidae) from French Guiana with a redescription of Colostethus beebei (Noble, 1923) from its type locality
Kok, Ph.J.R. ; MacCulloch, R.D. ; Gaucher, P. ; Poelman, E.H. ; Bourne, G.R. ; Lathrop, A. ; Lenglet, G.L. - \ 2006
Phyllomedusa 5 (2006)1. - ISSN 1519-1397 - p. 43 - 66.
A new species of Colostethus (Anura, Dendrobatidae) from French Guiana with a redescription of Colostethus beebei (Noble, 1923) from its type locality, a new species of Colostethus, long mistaken for Colostethus beebei, is described from French Guiana. The New species can be distinguished from congeners by absence of median lingual process, first finger longer than second, third finger not distinctly swollen in males, differences in tadpole morphology, coloration, and pattern (e.g. absence of dorsolateral stripe) bioacoustics, and reproducitve behavior. A complete redescription of Colotethus beebei, plus its tadpole and call is provided on the basis of recently collected topotypic specimens. The range of C. beebei is restricted to the Kaieteur plateau, Pakaraima, Guyana
Aspergillus niger protein estA defines a new class of fungal esterases within the alfa/beta hydrolase fold superfamily of proteins
Bourne, Y. ; Hasper, A.A. ; Chahinian, H. ; Juin, M. ; Graaff, L.H. de - \ 2004
Structure 12 (2004)8. - ISSN 0969-2126 - p. 677 - 687.
transcriptional activator xlnr - 3-dimensional structure - acetylxylan esterase - antifungal agents - gene-expression - vinyl esters - sequence - acetylcholinesterase - lipases - refinement
From the fungus Aspergillus niger, we identified a new gene encoding protein EstA, a member of the alpha/beta-hydrolase fold superfamily but of unknown substrate specificity. EstA was overexpressed and its crystal structure was solved by molecular replacement using a lipaseacetylcholinesterase chimera template. The 2.1 A resolution structure of EstA reveals a canonical Ser/Glu/ His catalytic triad located in a small pocket at the bottom of a large solvent-accessible, bowl-shaped cavity. Potential substrates selected by manual docking procedures were assayed for EstA activity. Consistent with the pocket geometry, preference for hydrolysis of short acyl/propyl chain substrates was found. Identification of close homologs from the genome of other fungi, of which some are broad host-range pathogens, defines EstA as the first member of a novel class of fungal esterases within the superfamily. Hence the structure of EstA constitutes a lead template in the design of new antifungal agents directed toward its pathogenic homologs.
Boekbespreking: Impact of nutrition on health and disease, G.H. Bourne (ed.). World Rev. Nutr. & Dietetics, Vol.59. Karger, Basel, 1989, 220 pp.
Staveren, W.A. van - \ 1992
Tijdschrift voor Gerontologie en Geriatrie 23 (1992). - ISSN 0167-9228 - p. 126 - 126.
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