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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Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep
Thomas, Nadine A. ; Olvera-Ramírez, Andrea M. ; Abecia, Leticia ; Adam, Clare L. ; Edwards, Joan E. ; Cox, Georgina F. ; Findlay, Patricia A. ; Destables, Elodie ; Wood, Tracy A. ; McEwan, Neil R. - \ 2019
Archives of Microbiology 201 (2019)7. - ISSN 0302-8933 - p. 889 - 896.
Anaerobic fungi - Bacteria - Ciliated protozoa - Day length - Digestive tract - Soay sheep

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

Potential for re-emergence of wheat stem rust in the United Kingdom
Lewis, Clare M. ; Persoons, Antoine ; Bebber, Daniel P. ; Kigathi, Rose N. ; Maintz, Jens ; Findlay, Kim ; Bueno-Sancho, Vanessa ; Corredor-Moreno, Pilar ; Harrington, Sophie A. ; Kangara, Ngonidzashe ; Berlin, Anna ; García, Richard ; Germán, Silvia E. ; Hanzalová, Alena ; Hodson, David P. ; Hovmøller, Mogens S. ; Huerta-Espino, Julio ; Imtiaz, Muhammed ; Mirza, Javed Iqbal ; Justesen, Annemarie F. ; Niks, Rients E. ; Omrani, Ali ; Patpour, Mehran ; Pretorius, Zacharias A. ; Roohparvar, Ramin ; Sela, Hanan ; Singh, Ravi P. ; Steffenson, Brian ; Visser, Botma ; Fenwick, Paul M. ; Thomas, Jane ; Wulff, Brande B.H. ; Saunders, Diane G.O. - \ 2018
Communications Biology 1 (2018)1. - ISSN 2399-3642

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK. Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.

How effective is road mitigation at reducing road-kill? A meta-analysis
Rytwinski, Trina ; Soanes, Kylie ; Jaeger, Jochen A.G. ; Fahrig, Lenore ; Findlay, C.S. ; Houlahan, Jeff ; Ree, Rodney van der; Grift, Edgar A. van der - \ 2016
PLoS ONE 11 (2016)11. - ISSN 1932-6203

Road traffic kills hundreds of millions of animals every year, posing a critical threat to the populations of many species. To address this problem there are more than forty types of road mitigation measures available that aim to reduce wildlife mortality on roads (road-kill). For road planners, deciding on what mitigation method to use has been problematic because there is little good information about the relative effectiveness of these measures in reducing road-kill, and the costs of these measures vary greatly. We conducted a metaanalysis using data from 50 studies that quantified the relationship between road-kill and a mitigation measure designed to reduce road-kill. Overall, mitigation measures reduce roadkill by 40% compared to controls. Fences, with or without crossing structures, reduce roadkill by 54%. We found no detectable effect on road-kill of crossing structures without fencing. We found that comparatively expensive mitigation measures reduce large mammal road-kill much more than inexpensive measures. For example, the combination of fencing and crossing structures led to an 83% reduction in road-kill of large mammals, compared to a 57% reduction for animal detection systems, and only a 1% for wildlife reflectors. We suggest that inexpensive measures such as reflectors should not be used until and unless their effectiveness is tested using a high-quality experimental approach. Our meta-analysis also highlights the fact that there are insufficient data to answer many of the most pressing questions that road planners ask about the effectiveness of road mitigation measures, such as whether other less common mitigation measures (e.g., measures to reduce traffic volume and/or speed) reduce road mortality, or to what extent the attributes of crossing structures and fences influence their effectiveness. To improve evaluations of mitigation effectiveness, studies should incorporate data collection before the mitigation is applied, and we recommend a minimum study duration of four years for Before-After, and a minimum of either four years or four sites for Before-After-Control-Impact designs.

Experimental study designs to improve the evaluation of road mitigation measures for wildlife
Rytwinski, T. ; Van der Ree, R. van der; Cunnington, G.M. ; Fahrig, L. ; Findlay, C.S. ; Houlahan, J. ; Jaeger, J.A.G. ; Soanes, K. ; Grift, E.A. van der - \ 2015
Journal of Environmental Management 154 (2015). - ISSN 0301-4797 - p. 48 - 64.
An experimental approach to road mitigation that maximizes inferential power is essential to ensure that mitigation is both ecologically-effective and cost-effective. Here, we set out the need for and standards of using an experimental approach to road mitigation, in order to improve knowledge of the influence of mitigation measures on wildlife populations. We point out two key areas that need to be considered when conducting mitigation experiments. First, researchers need to get involved at the earliest stage of the road or mitigation project to ensure the necessary planning and funds are available for conducting a high quality experiment. Second, experimentation will generate new knowledge about the parameters that influence mitigation effectiveness, which ultimately allows better prediction for future road mitigation projects. We identify seven key questions about mitigation structures (i.e., wildlife crossing structures and fencing) that remain largely or entirely unanswered at the population-level: (1) Does a given crossing structure work? What type and size of crossing structures should we use? (2) How many crossing structures should we build? (3) Is it more effective to install a small number of large-sized crossing structures or a large number of small-sized crossing structures? (4) How much barrier fencing is needed for a given length of road? (5) Do we need funnel fencing to lead animals to crossing structures, and how long does such fencing have to be? (6) How should we manage/manipulate the environment in the area around the crossing structures and fencing? (7) Where should we place crossing structures and barrier fencing? We provide experimental approaches to answering each of them using example Before-After-Control-Impact (BACI) study designs for two stages in the road/mitigation project where researchers may become involved: (1) at the beginning of a road/mitigation project, and (2) after the mitigation has been constructed; highlighting real case studies when available.
The Rauischholzhausen agenda for road ecology
Roedenbeck, I.A. ; Fahrig, L. ; Findlay, C.S. ; Houlahan, J.E. ; Jaeger, J.A.G. ; Klar, N. ; Kramer-Schadt, S. ; Grift, E.A. van der - \ 2007
Ecology and Society 12 (2007)1. - ISSN 1708-3087 - 21 p.
breeding bird populations - precautionary principle - environmental impacts - swareflex reflectors - sampling design - habitat - conservation - density - deer - biodiversity
Despite the documented negative effects of roads on wildlife, ecological research on road effects has had comparatively little influence on road planning decisions. We argue that road research would have a larger impact if researchers carefully considered the relevance of the research questions addressed and the inferential strength of the studies undertaken. At a workshop at the German castle of Rauischholzhausen we identified five particularly relevant questions, which we suggest provide the framework for a research agenda for road ecology: (1) Under what circumstances do roads affect population persistence? (2) What is the relative importance of road effects vs. other effects on population persistence? (3) Under what circumstances can road effects be mitigated? (4) What is the relative importance of the different mechanisms by which roads affect population persistence? (5) Under what circumstances do road networks affect population persistence at the landscape scale? We recommend experimental designs that maximize inferential strength, given existing constraints, and we provide hypothetical examples of such experiments for each of the five research questions. In general, manipulative experiments have higher inferential strength than do nonmanipulative experiments, and full before-after-control-impact designs are preferable to before-after or control-impact designs. Finally, we argue that both scientists and planners must be aware of the limits to inferential strength that exist for a given research question in a given situation. In particular, when the maximum inferential strength of any feasible design is low, decision makers must not demand stronger evidence before incorporating research results into the planning process, even though the level of uncertainty may be high
Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H+-ATPase
Duarte, A.M. ; Wolfs, C.J.A.M. ; Nuland, N.A.J. van; Harrison, M.A. ; Findlay, J.B.C. ; Mierlo, C.P.M. van; Hemminga, M.A. - \ 2007
Biochimica et Biophysica Acta. Biomembranes 1768 (2007)2. - ISSN 0005-2736 - p. 218 - 227.
nuclear-magnetic-resonance - sarcoplasmic-reticulum ca2+-atpase - protein secondary structure - circular-dichroism spectra - sodium dodecyl-sulfate - m13 coat protein - v-atpase - vacuolar (h+)-atpases - membrane-proteins - nmr-spectroscopy
Vacuolar (H+)-ATPase (V-ATPase) is a proton pump present in several compartments of eukaryotic cells to regulate physiological processes. From biochemical studies it is known that the interaction between arginine 735 present in the seventh transmembrane (TM7) segment from subunit a and specific glutamic acid residues in the subunit c assembly plays an essential role in proton translocation. To provide more detailed structural information about this protein domain, a peptide resembling TM7 (denoted peptide MTM7) from Saccharomyces cerevisiae (yeast) V-ATPase was synthesized and dissolved in two membrane-mimicking solvents: DMSO and SDS. For the first time the secondary structure of the putative TM7 segment from subunit a is obtained by the combined use of CD and NMR spectroscopy. SDS micelles reveal an ¿-helical conformation for peptide MTM7 and in DMSO three ¿-helical regions are identified by 2D 1H-NMR. Based on these conformational findings a new structural model is proposed for the putative TM7 in its natural environment. It is composed of 32 amino acid residues that span the membrane in an ¿-helical conformation. It starts at the cytoplasmic side at residue T719 and ends at the luminal side at residue W751. Both the luminal and cytoplasmatic regions of TM7 are stabilized by the neighboring hydrophobic transmembrane segments of subunit a and the subunit c assembly from V-ATPase
DIF1, a plant gene essential for meiosis has homology to a double stranded break repair protein.
Bhatt, A.M. ; Page, T. ; Lister, C. ; Findlay, K. ; Fransz, P. ; Jones, G.H. ; Dickinson, H.G. ; Dean, C. - \ 1997
In: Third European Conference on Meiosis, Wageningen - p. 8 - 8.
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