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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    Aerobic swimming in intensive finfish aquaculture : applications for production, mitigation and selection
    McKenzie, David J. ; Palstra, Arjan P. ; Planas, Josep ; MacKenzie, Simon ; Bégout, Marie Laure ; Thorarensen, Helgi ; Vandeputte, Marc ; Mes, Daan ; Rey, Sonia ; Boeck, Gudrun De; Domenici, Paolo ; Skov, Peter V. - \ 2020
    Reviews in Aquaculture (2020). - ISSN 1753-5123
    aerobic exercise - growth - maturation - selection - stress - welfare

    We review knowledge on applications of sustained aerobic swimming as a tool to promote productivity and welfare of farmed fish species. There has been extensive interest in whether providing active species with a current to swim against can promote growth. The results are not conclusive but the studies have varied in species, life stage, swimming speed applied, feeding regime, stocking density and other factors. Therefore, much remains to be understood about mechanisms underlying findings of ‘swimming-enhanced growth’, in particular to demonstrate that swimming can improve feed conversion ratio and dietary protein retention under true aquaculture conditions. There has also been research into whether swimming can alleviate chronic stress, once again on a range of species and life stages. The evidence is mixed but swimming does improve recovery from acute stresses such as handling or confinement. Research into issues such as whether swimming can improve immune function and promote cognitive function is still at an early stage and should be encouraged. There is promising evidence that swimming can inhibit precocious sexual maturation in some species, so studies should be broadened to other species where precocious maturation is a problem. Swimming performance is a heritable trait and may prove a useful selection tool, especially if it is related to overall robustness. More research is required to better understand the advantages that swimming may provide to the fish farmer, in terms of production, mitigation and selection.

    Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism
    Vink, Jochem N.A. ; Martens, Koen J.A. ; Vlot, Marnix ; McKenzie, Rebecca E. ; Almendros, Cristóbal ; Estrada Bonilla, Boris ; Brocken, Daan J.W. ; Hohlbein, Johannes ; Brouns, Stan J.J. - \ 2020
    Molecular Cell 77 (2020)1. - ISSN 1097-2765 - p. 39 - 50.e10.
    arms race - Cascade - CRISPR-Cas - PALM - PAM - photo-activation localization microscopy - single molecule - single-particle tracking - target search

    Vink et al. tracked single CRISPR RNA-surveillance complexes (Cascade) in the native host cell and determined the influence of Cascade copy numbers, PAM scanning speed, and the presence of CRISPR arrays and transcription on their ability to find and clear invading mobile genetic elements from the cell.

    Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation
    Almendros, Cristóbal ; Nobrega, Franklin L. ; McKenzie, Rebecca E. ; Brouns, Stan J.J. - \ 2019
    Nucleic acids research 47 (2019)10. - ISSN 0305-1048 - p. 5223 - 5230.

    Microbes have the unique ability to acquire immunological memories from mobile genetic invaders to protect themselves from predation. To confer CRISPR resistance, new spacers need to be compatible with a targeting requirement in the invader's DNA called the protospacer adjacent motif (PAM). Many CRISPR systems encode Cas4 proteins to ensure new spacers are integrated that meet this targeting prerequisite. Here we report that a gene fusion between cas4 and cas1 from the Geobacter sulfurreducens I-U CRISPR-Cas system is capable of introducing functional spacers carrying interference proficient TTN PAM sequences at much higher frequencies than unfused Cas4 adaptation modules. Mutations of Cas4-domain catalytic residues resulted in dramatically decreased naïve and primed spacer acquisition, and a loss of PAM selectivity showing that the Cas4 domain controls Cas1 activity. We propose the fusion gene evolved to drive the acquisition of only PAM-compatible spacers to optimize CRISPR interference.

    Using CAPTURE to detect spacer acquisition in native CRISPR arrays
    McKenzie, Rebecca E. ; Almendros, Cristóbal ; Vink, Jochem N.A. ; Brouns, Stan J.J. - \ 2019
    Nature protocols (2019)14. - ISSN 1754-2189 - p. 976 - 990.

    CRISPR–Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection; however, this often occurs at low frequency within a population, which can make it difficult to detect. Here we describe CAPTURE (CRISPR adaptation PCR technique using reamplification and electrophoresis), a versatile and adaptable protocol to detect spacer-acquisition events by electrophoresis imaging with high-enough sensitivity to identify spacer acquisition in 1 in 10 5 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, thus allowing the removal of unexpanded arrays from the sample pool and enabling 1,000-times more sensitive detection of new spacers than alternative PCR protocols. CAPTURE is a straightforward method that requires only 1 d to enable the detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unraveling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.

    Role of nucleotide identity in effective CRISPR target escape mutations
    Künne, Tim ; Zhu, Yifan ; Silva, Fausia da; Konstantinides, Nico ; McKenzie, Rebecca E. ; Jackson, Ryan N. ; Brouns, Stan J.J. - \ 2018
    Nucleic acids research 46 (2018)19. - ISSN 0305-1048 - p. 10395 - 10404.

    Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR-Cas systems.

    Maternal circulating vitamin status and colostrum vitamin composition in healthy lactating women—A systematic approach
    Vries, Jasmijn Y. de; Pundir, Shikha ; McKenzie, Elizabeth ; Keijer, Jaap ; Kussmann, Martin - \ 2018
    Nutrients 10 (2018)6. - ISSN 2072-6643
    Colostrum - Human milk - Infant - Plasma - Vitamins

    Colostrum is the first ingested sole nutritional source for the newborn infant. The vitamin profile of colostrum depends on the maternal vitamin status, which in turn is influenced by diet and lifestyle. Yet, the relationship between maternal vitamin status and colostrum vitamin composition has not been systematically reviewed. This review was conducted with the aim to generate a comprehensive overview on the relationship between maternal serum (plasma) vitamin concentration and corresponding colostrum composition. Three electronic databases, Embase (Ovid), Medline (Ovid), and Cochrane, were systematically searched based on predefined inclusion and exclusion criteria. Finally, a total of 11 eligible publications were included that examined the vitamins A, C, D, E, and K in both biological fluids. Maternal vitamin A, D, E, and K blood levels were unrelated to colostrum content of the respective vitamins, and serum vitamin A was inversely correlated with colostrum vitamin E. Colostrum versus maternal serum vitamins were higher for vitamins A, C, and K, lower for vitamin D, and divergent results were reported for vitamin E levels. Colostrum appears typically enriched in vitamin A, C, and K compared to maternal serum, possibly indicative of active mammary gland transport mechanisms. Inter-individual and inter-study high variability in colostrum’s vitamin content endorses its sensitivity to external factors.

    Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation
    Kieper, Sebastian N. ; Almendros, Cristóbal ; Behler, Juliane ; McKenzie, Rebecca E. ; Nobrega, Franklin L. ; Haagsma, Anna C. ; Vink, Jochem N.A. ; Hess, Wolfgang R. ; Brouns, Stan J.J. - \ 2018
    Cell Reports 22 (2018)13. - ISSN 2211-1247 - p. 3377 - 3384.
    Cas4 - CRISPR adaptation - spacer acquisition - type I-D CRISPR-Cas system
    CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Kieper et al. demonstrate that the ubiquitous protein Cas4 assists Cas1 and Cas2 in the selection of new CRISPR spacers with a PAM licensing efficient CRISPR interference.
    Groundwater flow and heat transport for systems undergoing freeze-thaw : Intercomparison of numerical simulators for 2D test cases
    Grenier, Christophe ; Anbergen, Hauke ; Bense, Victor ; Chanzy, Quentin ; Coon, Ethan ; Collier, Nathaniel ; Costard, François ; Ferry, Michel ; Frampton, Andrew ; Frederick, Jennifer ; Gonçalvès, Julio ; Holmén, Johann ; Jost, Anne ; Kokh, Samuel ; Kurylyk, Barret ; McKenzie, Jeffrey ; Molson, John ; Mouche, Emmanuel ; Orgogozo, Laurent ; Pannetier, Romain ; Rivière, Agnès ; Roux, Nicolas ; Rühaak, Wolfram ; Scheidegger, Johanna ; Selroos, Jan Olof ; Therrien, René ; Vidstrand, Patrik ; Voss, Clifford - \ 2018
    Advances in Water Resources 114 (2018). - ISSN 0309-1708 - p. 196 - 218.
    Code benchmarking - Numerical simulation - Permafrost - Sharp interface problems - Thermo-hydrological coupling
    In high-elevation, boreal and arctic regions, hydrological processes and associated water bodies can be strongly influenced by the distribution of permafrost. Recent field and modeling studies indicate that a fully-coupled multidimensional thermo-hydraulic approach is required to accurately model the evolution of these permafrost-impacted landscapes and groundwater systems. However, the relatively new and complex numerical codes being developed for coupled non-linear freeze-thaw systems require verification. This issue is addressed by means of an intercomparison of thirteen numerical codes for two-dimensional test cases with several performance metrics (PMs). These codes comprise a wide range of numerical approaches, spatial and temporal discretization strategies, and computational efficiencies. Results suggest that the codes provide robust results for the test cases considered and that minor discrepancies are explained by computational precision. However, larger discrepancies are observed for some PMs resulting from differences in the governing equations, discretization issues, or in the freezing curve used by some codes.
    Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
    O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
    Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
    Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
    Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
    GlobalSoilMap for Soil Organic Carbon Mapping and as a Basis for Global Modeling
    Arrouays, D. ; Minasny, B. ; McBratney, A. ; Grundy, Mike ; McKenzie, Neil ; Thompson, James ; Gimona, Alessandro ; Hong, Suk Young ; Smith, Scott ; Hartemink, A.E. ; Chen, Songchao ; Martin, Manuel P. ; Mulder, V.L. ; Richer-de-Forges, A.C. ; Odeh, Inakwu ; Padarian, José ; Lelyk, Glenn ; Poggio, Laura ; Savin, Igor ; Stolbovoy, Vladimir ; Leenaars, J.G.B. ; Heuvelink, G.B.M. ; Montanarella, Luca ; Panagos, P. ; Hempel, Jon - \ 2017
    In: Proceedings of the global symposium on soil organic carbon 2017. - FAO - p. 27 - 30.
    The demand for information on functional soil properties is high and has increased over time. This is especially true for soil organic carbon (SOC) in the framework of food security and climate change. The GlobalSoilMap consortium was established in response to such a soaring demand for up-to-date and relevant soil information. The majority of the data needed to produce GlobalSoilMap soil property maps will, at least for the first generation, come mainly from archived soil legacy data, which could include polygon soil maps and point pedon data, and from available co-variates such as climatic data, remote sensing information, geological data, and other forms of environmental information.
    Several countries have already released products according to the GlobalSoilMap specifications and the project is rejuvenating soil survey and mapping in many parts of the world. Functional soil property maps have been produced using digital soil mapping techniques and existing legacy information and made available to the user community for application. In addition, uncertainty has been provided as a 90% prediction interval based on estimated upper and lower class limits. We believe that GlobalSoilMap constitutes the best available framework and methodology to address global issues about SOC mapping. Main scientific challenges include time related and uncertainties issues.
    CRISPR-Cas : Adapting to change
    Jackson, Simon A. ; McKenzie, Rebecca E. ; Fagerlund, Robert D. ; Kieper, Sebastian N. ; Fineran, Peter C. ; Brouns, Stan J.J. - \ 2017
    Science 356 (2017)6333. - ISSN 0036-8075
    Bacteria and archaea are engaged in a constant arms race to defend against the ever-present threats of viruses and invasion by mobile genetic elements. The most flexible weapons in the prokaryotic defense arsenal are the CRISPR-Cas adaptive immune systems. These systems are capable of selective identification and neutralization of foreign DNA and/or RNA. CRISPR-Cas systems rely on stored genetic memories to facilitate target recognition. Thus, to keep pace with a changing pool of hostile invaders, the CRISPR memory banks must be regularly updated with new information through a process termed CRISPR adaptation. In this Review, we outline the recent advances in our understanding of the molecular mechanisms governing CRISPR adaptation. Specifically, the conserved protein machinery Cas1-Cas2 is the cornerstone of adaptive immunity in a range of diverse CRISPR-Cas systems.
    Conservation physiology of marine fishes: state of the art and prospects for policy
    Mckenzie, David J. ; Axelsson, Michael ; Chabot, Denis ; Claireaux, Guy ; Cooke, Steven J. ; Corner, Richard A. ; Boeck, Gudrun De; Domenici, Paolo ; Guerreiro, Pedro M. ; Hamer, Bojan ; Jørgensen, Christian ; Killen, Shaun S. ; Lefevre, Sjannie ; Marras, Stefano ; Michaelidis, Basile ; Nilsson, Göran E. ; Peck, Myron A. ; Perez-Ruzafa, Angel ; Rijnsdorp, Adriaan D. ; Shiels, Holly A. ; Steffensen, John F. ; Svendsen, Jon C. ; Svendsen, Morten B.S. ; Teal, Lorna R. ; Meer, Jaap Van Der; Wang, Tobias ; Wilson, Jonathan M. ; Wilson, Rod W. ; Metcalfe, Julian D. - \ 2016
    Conservation Physiology 4 (2016)1. - ISSN 2051-1434
    Biomarkers - ecological models - fisheries - Fry paradigm - individual variation - telemetry
    The state of the art of research on the environmental physiology of marine fishes is reviewed from the perspective of how it can contribute to conservation of knowledge for conservation of marine fishes is the limited knowledge base; international collaboration is needed to study the environmental physiology of a wider range of species. Multifactorial field and laboratory studies on biomarkers hold promise to relate ecophysiology directly to habitat quality and population status. The ‘Fry paradigm’ could have broad applications for conservation physiology research if it provides a universal mechanism to link physiological function with ecological performance and population dynamics of fishes, through effects of abiotic conditions on aerobic metabolic scope. The available data indicate, however, that the paradigm is not universal, so further research is required on a wide diversity of species. Fish physiologists should interact closely with researchers developing ecological models, in order to investigate how integrating physiological information improves confidence in projecting effects of global change; for example, with mechanistic models that define habitat suitability based upon potential for aerobic scope or outputs of a dynamic energy budget. One major challenge to upscaling from physiology of individuals to the level of species and communities is incorporating intraspecific variation, which could be a crucial component of species’ resilience to global change.
    Understanding what fishes do in the wild is also a challenge, but techniques of novel information towards effective conservation. Overall, fish physiologists must strive to render research outputs more applicable to management and decision-making. There are various potential avenues for information flow, in the shorter term directly through biomarker studies and in the longer term by collaborating with modellers and fishery biologists.
    Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system
    Wilkinson, Max E. ; Nakatani, Yoshio ; Staals, Raymond H.J. ; Kieper, Sebastian N. ; Opel-Reading, Helen K. ; McKenzie, Rebecca E. ; Fineran, Peter C. ; Krause, Kurt L. - \ 2016
    Biochemical Journal 473 (2016)8. - ISSN 0264-6021 - p. 1063 - 1072.
    Adaptation - Bacteriophages - Csy - Horizontal gene transfer - Plasmids - Protein structure

    CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

    Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer
    Richter, Corinna ; Dy, Ron L. ; McKenzie, Rebecca E. ; Watson, Bridget N.J. ; Taylor, Corinda ; Chang, James T. ; McNeil, Matthew B. ; Staals, Raymond H.J. ; Fineran, Peter C. - \ 2014
    Nucleic acids research 42 (2014)13. - ISSN 0305-1048 - p. 8516 - 8526.

    Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼350 new spacers acquired in priming events and identified a 5′-protospacer-GG-3′ protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2-3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.

    Comparing spatial prediction methods for soil property mapping in Brazil: a case study for the Rio Doce Basin
    Souza, E. de; Hengl, T. ; Kempen, B. ; Heuvelink, G.B.M. ; Fernandes Filho, E.I. ; Schaefer, C.E.G.R. - \ 2014
    In: GlobalSoilMap: Basis of the Global Spatial Soil Information System. - Orléans : Taylor & Francis - ISBN 9781315775586 - p. 267 - 271.
    Towards products for the Netherlands
    Kempen, B. ; Brus, D.J. ; Heuvelink, G.B.M. ; Walvoort, D.J.J. - \ 2014
    In: GlobalSoilMap: Basis of the Global Spatial Soil Information System. - Orléans : Taylor & Francis - ISBN 9781138001190 - p. 85 - 90.
    One stop shop: backbones trees for important phytopathogenic genera: I (2014)
    Hyde, K.D. ; Nilsson, R.H. ; Alias, S.A. ; Ariyawansa, H.A. ; Blair, J.E. ; Cai, L. ; Cock, A.W.A.M. de; Dissanayake, A.J. ; Glockling, S.L. ; Goonasekara, I.D. ; Gorczak, M. ; Hahn, M. ; Jayawardena, R.S. ; Kan, J.A.L. van; Laurence, M.H. ; Lévesque, C.A. ; Li, X. ; Liu, J.K. ; Maharachchikumbura, S.S.N. ; Manamgoda, D.S. ; Martin, F.N. ; McKenzie, E.H.C. ; McTaggart, A.R. ; Mortimer, P.E. ; Nair, P.V.R. ; Pawlowska, J. ; Rintoul, T.L. ; Shivas, R.G. ; Spies, C.F.J. ; Summerell, B.A. ; Taylor, P.W.J. ; Terhem, R.B. ; Udayanga, D. ; Vaghefi, N. ; Walther, G. ; Wilk, M. ; Wrzosek, M. ; Xu, J.C. ; Yan, J.Y. ; Zhou, N. - \ 2014
    Fungal Diversity 67 (2014). - ISSN 1560-2745 - p. 21 - 125.
    internal transcribed spacer - ribosomal dna-sequences - vegetative compatibility groups - plant-pathogenic fungi - citrus black spot - spored graminicolous colletotrichum - sporisorium-macalpinomyces complex - fragment-length-polymorphisms - botrytis-cinerea popu
    Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
    Cross-cultural color-odor associations
    Levitan, C.A. ; Ren, J. ; Boesveldt, S. ; Chan, J. ; McKenzie, K.J. ; Levin, J.A. ; Leong, C.X. ; Bosch, J.F. van den - \ 2014
    PLoS ONE 9 (2014)7. - ISSN 1932-6203
    modal associations - perception - correspondences - olfaction - responses - language - emotion - scents - smell
    Colors and odors are associated; for instance, people typically match the smell of strawberries to the color pink or red. These associations are forms of crossmodal correspondences. Recently, there has been discussion about the extent to which these correspondences arise for structural reasons (i.e., an inherent mapping between color and odor), statistical reasons (i.e., covariance in experience), and/or semantically-mediated reasons (i.e., stemming from language). The present study probed this question by testing color-odor correspondences in 6 different cultural groups (Dutch, Netherlands-residing-Chinese, German, Malay, Malaysian-Chinese, and US residents), using the same set of 14 odors and asking participants to make congruent and incongruent color choices for each odor. We found consistent patterns in color choices for each odor within each culture, showing that participants were making non-random color-odor matches. We used representational dissimilarity analysis to probe for variations in the patterns of color-odor associations across cultures; we found that US and German participants had the most similar patterns of associations, followed by German and Malay participants. The largest group differences were between Malay and Netherlands-resident Chinese participants and between Dutch and Malaysian-Chinese participants. We conclude that culture plays a role in color-odor crossmodal associations, which likely arise, at least in part, through experience.
    Prion disease tempo determined by host-dependent substrate reduction
    Mays, C.E. ; Kim, C. ; Haldiman, T. ; Merwe, J. v.d.; Lau, A. ; Yang, J. ; Grams, J. ; Bari, M.A. Di; Nonno, R. ; Telling, G.C. ; Kong, Q. ; Langeveld, J.P.M. ; McKenzie, D. ; Westaway, D. ; Safar, J.G. - \ 2014
    The Journal of Clinical Investigation 124 (2014)2. - ISSN 0021-9738 - p. 847 - 858.
    chronic wasting disease - transgenic mice - cyclic amplification - cultured-cells - sheep scrapie - prpsc levels - protein - propagation - immunoassay - strains
    The symptoms of prion infection can take years or decades to manifest following the initial exposure. Molecular markers of prion disease include accumulation of the misfolded prion protein (PrPSc), which is derived from its cellular precursor (PrPC), as well as downregulation of the PrP-like Shadoo (Sho) glycoprotein. Given the overlapping cellular environments for PrPC and Sho, we inferred that PrPC levels might also be altered as part of a host response during prion infection. Using rodent models, we found that, in addition to changes in PrPC glycosylation and proteolytic processing, net reductions in PrPC occur in a wide range of prion diseases, including sheep scrapie, human Creutzfeldt-Jakob disease, and cervid chronic wasting disease. The reduction in PrPC results in decreased prion replication, as measured by the protein misfolding cyclic amplification technique for generating PrPSc in vitro. While PrPC downregulation is not discernible in animals with unusually short incubation periods and high PrPC expression, slowly evolving prion infections exhibit downregulation of the PrPC substrate required for new PrPSc synthesis and as a receptor for pathogenic signaling. Our data reveal PrPC downregulation as a previously unappreciated element of disease pathogenesis that defines the extensive, presymptomatic period for many prion strains
    S-world: A global map of soil properties for modelling
    Stoorvogel, J.J. - \ 2014
    In: Proceedings of the 1st GlobalSoilMap Conference on GlobalSoilMap: Basis of the global spatial soil information system, Orleans, France, 7 - 9 October 2013. - London, UK : Taylor & Francis - ISBN 9781138001190 - p. 227 - 231.
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