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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DeepGlobe 2018: A Challenge to Parse the Earth through Satellite Images
Demir, I. ; Koperski, K. ; Lindenbaum, D. ; Pang, G. ; Huang, J. ; Basu, S. ; Hughes, F. ; Tuia, D. ; Raska, R. - \ 2018
In: Proceedings 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops CVPRW 2018. - IEEE - ISBN 9781538661017 - p. 17200 - 17209.
We present the DeepGlobe 2018 Satellite Image Understanding Challenge, which includes three public competitions for segmentation, detection, and classification tasks on satellite images (Figure 1). Similar to other challenges in computer vision domain such as DAVIS[21] and COCO[33], DeepGlobe proposes three datasets and corresponding evaluation methodologies, coherently bundled in three competitions with a dedicated workshop co-located with CVPR 2018. We observed that satellite imagery is a rich and structured source of information, yet it is less investigated than everyday images by computer vision researchers. However, bridging modern computer vision with remote sensing data analysis could have critical impact to the way we understand our environment and lead to major breakthroughs in global urban planning or climate change research. Keeping such bridging objective in mind, DeepGlobe aims to bring together researchers from different domains to raise awareness of remote sensing in the computer vision community and vice-versa. We aim to improve and evaluate state-of-the-art satellite image understanding approaches, which can hopefully serve as reference benchmarks for future research in the same topic. In this paper, we analyze characteristics of each dataset, define the evaluation criteria of the competitions, and provide baselines for each task.
Benefits and costs of livestock systems in ten European case studies
Neumeister, D. ; Zehetmeier, M. ; Olde, E.M. de; Valada, T. ; Tichit, M. ; Rodriguezo, T. ; Morgan-Davis, C. ; Boer, I.J.M. de; Perrot, C. ; Dockes, A.C. - \ 2018
In: Book of abstracts of the 69th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 24) - ISBN 9789086863235 - p. 253 - 253.
Innovation platforms in agricultural research development : Ex-ante Appraisal of the Purposes and Conditions Under Which Innovation Platforms can Contribute to Agricultural Development Outcomes
Schut, Marc ; Kamanda, Josey ; Gramzow, Andreas ; Dubois, Thomas ; Stoian, Dietmar ; Andersson, Jens A. ; Dror, Iddo ; Sartas, Murat ; Mur, Remco ; Kassam, Shinan ; Brouwer, Herman ; Devaux, André ; Velasco, Claudio ; Flor, Rica Joy ; Gummert, Martin ; Buizer, Djuna ; Mcdougall, Cynthia ; Davis, Kristin ; Tui, Sabine Homann-Kee ; Lundy, Mark - \ 2018
Experimental Agriculture (2018). - ISSN 0014-4797 - 22 p.
Innovation platforms are fast becoming part of the mantra of agricultural research for development projects and programmes. Their basic tenet is that stakeholders depend on one another to achieve agricultural development outcomes, and hence need a space where they can learn, negotiate and coordinate to overcome challenges and capture opportunities through a facilitated innovation process. Although much has been written on how to implement and facilitate innovation platforms efficiently, few studies support ex-ante appraisal of when and for what purpose innovation platforms provide an appropriate mechanism for achieving development outcomes, and what kinds of human and financial resource investments and enabling environments are required. Without these insights, innovation platforms run the risk of being promoted as a panacea for all problems in the agricultural sector. This study makes clear that not all constraints will require innovation platforms and, if there is a simpler and cheaper alternative, that should be considered first. Based on the review of critical design principles and plausible outcomes of innovation platforms, this study provides a decision support tool for research, development and funding agencies that can enhance more critical thinking about the purposes and conditions under which innovation platforms can contribute to achieving agricultural development outcomes.
HEx : A heterologous expression platform for the discovery of fungal natural products
Harvey, Colin J.B. ; Tang, Mancheng ; Schlecht, Ulrich ; Horecka, Joe ; Fischer, Curt R. ; Lin, Hsiao Ching ; Li, Jian ; Naughton, Brian ; Cherry, James ; Miranda, Molly ; Li, Yong Fuga ; Chu, Angela M. ; Hennessy, James R. ; Vandova, Gergana A. ; Inglis, Diane ; Aiyar, Raeka S. ; Steinmetz, Lars M. ; Davis, Ronald W. ; Medema, Marnix H. ; Sattely, Elizabeth ; Khosla, Chaitan ; Onge, Robert P.S. ; Tang, Yi ; Hillenmeyer, Maureen E. - \ 2018
Science Advances 4 (2018)4. - ISSN 2375-2548
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.
The Perspective of the Instruments : Mediating Collectivity
Boer, Bas de; Molder, Hedwig Te; Verbeek, Peter Paul - \ 2018
Foundations of Science 23 (2018)4. - ISSN 1233-1821 - p. 739 - 755.
Actor-Network Theory - Postphenomenology - Scientific instruments - Scientific Perspectivism - Technological mediation - Thing knowledge
Numerous studies in the fields of Science and Technology Studies (STS) and philosophy of technology have repeatedly stressed that scientific practices are collective practices that crucially depend on the presence of scientific technologies. Postphenomenology is one of the movements that aims to draw philosophical conclusions from these observations through an analysis of human–technology interactions in scientific practice. Two other attempts that try to integrate these insights into philosophy of science are Ronald Giere’s Scientific Perspectivism (2006) and Davis Baird’s Thing Knowledge (2004). In this paper, these two approaches will be critically discussed from the perspective of postphenomenology. We will argue that Giere and Baird problematically assume that scientific instruments (a) have a determined function, and (b) that all human members of a scientific collective have immediate access to this function. However, these assumptions also allow them to offer a clear answer to the question how scientists can collectively relate to scientific phenomena. Such an answer is not yet (explicitly) formulated within the postphenomenological perspective. By adding a postphenomenological touch to the semiotic approach in Actor-Network Theory, we offer an account of how different individual human–technology relations are integrated into larger scientific collectives. We do so by showing that scientific instruments not only help constitute scientific phenomena, but also the intersubjectivity within such collectives.
Genetic characterization of clavibacter michiganensis subsp. Michiganensis population in Turkey
Sen, Yusuf ; Aysan, Yesim ; Mirik, Mustafa ; Ozdemir, Duygu ; Meijer-Dekens, Fien ; Wolf, Jan M. van der; Visser, Richard G.F. ; Heusden, Sjaak van - \ 2018
Plant Disease 102 (2018)2. - ISSN 0191-2917 - p. 300 - 308.
The pathogenic gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Smith) Davis et al. is the most harmful bacterium to tomatoes in many countries with a cooler climate. Multilocus sequence analysis was performed on five housekeeping genes (bipA, gyrB, kdpA, ligA, and sdhA) and three virulence-related genes (ppaA, chpC, andtomA) todetermine evolutionary relationships and population structure of 108 C. michiganensis subsp. michiganensis strains collected from Turkey between 1996 and 2012. Based on these analyses, we concluded that C. michiganensis subsp. michiganensis in Turkey is highly uniform. However, at least four novel C. michiganensis subsp. michiganensis strains were recently introduced, possibly at the beginning of the 1990s. The singletons might point to additional sources or to strains that have evolved locally in Turkey.
Updated measurements in vineyards improves accuracy of soil erosion rates
Rodrigo-Comino, Jesús ; Davis, Jason ; Keesstra, Saskia D. ; Cerdà, Artemi - \ 2018
Agronomy Journal 110 (2018)1. - ISSN 0002-1962 - p. 411 - 417.
All rights reserved. Vineyards have proven to be one of the most degraded agricultural ecosystems due to very high erosion rates, which are typically measured at fine temporal and spatial scales. Long-term soil erosion measures are rare, but this information may be indispensable for a proper understanding of the vineyard soil system, landscape evolution, and crop production. The stock unearthing method (SUM) is a common topographical measurement technique developed to assess long-term erosion rates. The reliance of the SUM has been questioned and should be replaced by an improved measurement technique. In this paper, we demonstrate the added value (improved accurate, low cost, and faster than photogrammetrically methods) of the improved stock unearthing method (ISUM). It was shown that large errors may have been made in previous assessments of soil erosion on vineyards, as the old method did not make measurements in the inter-row area or consider the timing of the erosion assessment in relation to tillage events. We found that this caused the SUM to severely underestimate soil erosion rates by –14.2 and –37.8% in 1- and 86-d tillage vineyards in one location, respectively. Furthermore, the increased measurement resolution attained from the ISUM allowed for the detailed assessment of micro-topographical change. Soil loss maps were able to detect the locational ch anges in soil depletion and accumulation, as well as continuous soil movement features in the inter-row areas. Ultimately, this leads to a more accurate estimate of the actual soil erosion rates in vineyards.
Non-Chemical Weed Management
Melander, Bo ; Liebman, Matt ; Davis, Adam S. ; Gallandt, Eric R. ; Bàrberi, Paolo ; Moonen, Anna Camilla ; Rasmussen, Jesper ; Weide, Rommie van der; Vidotto, Francesco - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley - ISBN 9781119969143 - p. 245 - 270.
Crop competition - Cultural methods - European weed research - Non-chemical weed management - North America - Organic crop production - Weed control methods - Weed germination

Non-chemical weed management covers all management practices that influence weeds except herbicides. This chapter summarises the major achievements in European research, as well as work undertaken in North America. Research groups from both continents have interacted strongly on the topic over the years and shared common interests on the development of non-chemical tactics. The chapter encompasses preventive, cultural and direct weed control methods, explaining the basic principles and the integration of these tactics in weed management strategies for agricultural and horticultural crops and in some cases amenity areas as well. Preventive methods reduce weed germination, cultural methods improve crop competition and direct physical weed control reduces weed survival. Non-chemical weed management is mainly adopted in organic crop production, as conventional growers still perceive it as more costly and less reliable than herbicide-based weed control programmes.

Use of Repeated Blood Pressure and Cholesterol Measurements to Improve Cardiovascular Disease Risk Prediction : An Individual-Participant-Data Meta-Analysis
Paige, Ellie ; Barrett, Jessica ; Pennells, Lisa ; Sweeting, Michael ; Willeit, Peter ; Angelantonio, Emanuele Di; Gudnason, Vilmundur ; Nordestgaard, Børge G. ; Psaty, Bruce M. ; Goldbourt, Uri ; Best, Lyle G. ; Assmann, Gerd ; Salonen, Jukka T. ; Nietert, Paul J. ; Verschuren, W.M.M. ; Brunner, Eric J. ; Kronmal, Richard A. ; Salomaa, Veikko ; Bakker, Stephan L.J. ; Dagenais, Gilles R. ; Sato, Shinichi ; Jansson, Jan Håkan ; Willeit, Johann ; Onat, Altan ; La Cámara, Agustin Gómez De; Roussel, Ronan ; Völzke, Henry ; Dankner, Rachel ; Tipping, Robert W. ; Meade, Tom W. ; Donfrancesco, Chiara ; Kuller, Lewis H. ; Peters, Annette ; Gallacher, John ; Kromhout, Daan ; Iso, Hiroyasu ; Knuiman, Matthew W. ; Casiglia, Edoardo ; Kavousi, Maryam ; Palmieri, Luigi ; Sundström, Johan ; Davis, Barry R. ; Njølstad, Inger ; Couper, David ; Danesh, John ; Thompson, Simon G. ; Wood, Angela M. - \ 2017
American Journal of Epidemiology 186 (2017)8. - ISSN 0002-9262 - p. 899 - 907.
Cardiovascular disease - Longitudinal measurements - Repeated measurements - Risk factors - Risk prediction
The added value of incorporating information from repeated blood pressure and cholesterol measurements to predict cardiovascular disease (CVD) risk has not been rigorously assessed. We used data on 191,445 adults from the Emerging Risk Factors Collaboration (38 cohorts from 17 countries with data encompassing 1962-2014) with more than 1 million measurements of systolic blood pressure, total cholesterol, and high-density lipoprotein cholesterol. Over a median 12 years of follow-up, 21,170 CVD events occurred. Risk prediction models using cumulative mean values of repeated measurements and summary measures from longitudinal modeling of the repeated measurements were compared with models using measurements from a single time point. Risk discrimination (Cindex) and net reclassification were calculated, and changes in C-indices were meta-analyzed across studies. Compared with the single-time-point model, the cumulative means and longitudinal models increased the C-index by 0.0040 (95% confidence interval (CI): 0.0023, 0.0057) and 0.0023 (95% CI: 0.0005, 0.0042), respectively. Reclassification was also improved in both models; compared with the single-time-point model, overall net reclassification improvements were 0.0369 (95% CI: 0.0303, 0.0436) for the cumulative-means model and 0.0177 (95% CI: 0.0110, 0.0243) for the longitudinal model. In conclusion, incorporating repeated measurements of blood pressure and cholesterol into CVD risk prediction models slightly improves risk prediction.
Strategies to Improve Stroke Care Services in Low- and Middle-Income Countries : A Systematic Review
Pandian, J.D. ; William, Akanksha G. ; Kate, Mahesh P. ; Norrving, Bo ; Mensah, George A. ; Davis, Stephen ; Roth, Gregory A. ; Thrift, Amanda G. ; Kengne, Andre P. ; Kissela, Brett M. ; Yu, Chuanhua ; Kim, Daniel ; Rojas-Rueda, David ; Tirschwell, David L. ; Abd-Allah, Foad ; Gankpé, Fortuné ; Deveber, Gabrielle ; Hankey, Graeme J. ; Jonas, Jost B. ; Sheth, Kevin N. ; Dokova, Klara ; Mehndiratta, Man Mohan ; Geleijnse, Johanna M. ; Giroud, Maurice ; Bejot, Yannick ; Sacco, Ralph ; Sahathevan, Ramesh ; Hamadeh, Randah Ribhi ; Gillum, Richard F. ; Westerman, Ronny ; Akinyemi, Rufus Olusola ; Barker-Collo, Suzanne ; Truelsen, Thomas ; Caso, Valeria ; Rajagopalan, Vasanthan ; Venketasubramanian, Narayanaswamy ; Vlassovi, Vasiliy V. ; Feigin, Valery L. - \ 2017
Neuroepidemiology 49 (2017)1-2. - ISSN 0251-5350 - p. 45 - 61.

Background: The burden of stroke in low- and middle-income countries (LMICs) is large and increasing, challenging the already stretched health-care services. Aims and Objectives: To determine the quality of existing stroke-care services in LMICs and to highlight indigenous, inexpensive, evidence-based implementable strategies being used in stroke-care. Methods: A detailed literature search was undertaken using PubMed and Google scholar from January 1966 to October 2015 using a range of search terms. Of 921 publications, 373 papers were shortlisted and 31 articles on existing stroke-services were included. Results: We identified efficient models of ambulance transport and pre-notification. Stroke Units (SU) are available in some countries, but are relatively sparse and mostly provided by the private sector. Very few patients were thrombolysed; this could be increased with telemedicine and governmental subsidies. Adherence to secondary preventive drugs is affected by limited availability and affordability, emphasizing the importance of primary prevention. Training of paramedics, care-givers and nurses in post-stroke care is feasible. Conclusion: In this systematic review, we found several reports on evidence-based implementable stroke services in LMICs. Some strategies are economic, feasible and reproducible but remain untested. Data on their outcomes and sustainability is limited. Further research on implementation of locally and regionally adapted stroke-services and cost-effective secondary prevention programs should be a priority.

Isolation by oceanic distance and spatial genetic structure in an overharvested international fishery
Truelove, Nathan K. ; Box, Stephen J. ; Aiken, Karl A. ; Blythe-Mallett, Azra ; Boman, Erik M. ; Booker, Catherine J. ; Byfield, Tamsen T. ; Cox, Courtney E. ; Davis, Martha H. ; Delgado, Gabriel A. ; Glazer, Bob A. ; Griffiths, Sarah M. ; Kitson-Walters, Kimani ; Kough, Andy S. ; Pérez Enríquez, Ricardo ; Preziosi, Richard F. ; Roy, Marcia E. ; Segura-García, Iris ; Webber, Mona K. ; Stoner, Allan W. - \ 2017
Diversity and Distributions 23 (2017)11. - ISSN 1366-9516 - p. 1292 - 1300.
Connectivity - Conservation - Dispersal - Fisheries - Genetics - Spatial

Aim: A detailed understanding of spatial genetic structure (SGS) and the factors driving contemporary patterns of gene flow and genetic diversity are fundamental for developing conservation and management plans for marine fisheries. We performed a detailed study of SGS and genetic diversity throughout the overharvested queen conch (Lobatus gigas) fishery. Caribbean countries were presented as major populations to examine transboundary patterns of population differentiation. Location: Nineteen locations in the greater Caribbean from Anguilla, the Bahamas, Belize, Caribbean Netherlands, Honduras, Jamaica, Mexico, Turks and Caicos, and the USA. Methods: We genotyped 643 individuals with nine microsatellites. Population genetic and multivariate analyses characterized SGS. We tested the alternate hypotheses: (1) SGS is randomly distributed in space or (2) pairwise genetic structure among sites is correlated with oceanic distance (IBOD). Results: Our study found that L. gigas does not form a single panmictic population in the greater Caribbean. Significant levels of genetic differentiation were identified between Caribbean countries (FCT = 0.011; p = .0001), within Caribbean countries (FSC = 0.003; p = .001), and among sites irrespective of geographic location (FST = 0.013; p = .0001). Gene flow across the greater Caribbean was constrained by oceanic distance (p = .0009; Mantel r = .40), which acted to isolate local populations. Main conclusions: Gene flow over the spatial scale of the entire Caribbean basin is constrained by oceanic distance, which may impede the natural recovery of overfished L. gigas populations. Our results suggest a careful blend of local and international management will be required to ensure long-term sustainability for the species.

Rapid Buffer and Ligand Screening for Affinity Chromatography by Multiplexed Surface Plasmon Resonance Imaging
Geuijen, K.P.M. ; Wijk-Basten, Danielle E.J.W. van; Egging, Davis F. ; Schasfoort, Richard B.M. ; Eppink, M.H.M. - \ 2017
Biotechnology Journal 12 (2017). - ISSN 1860-6768 - 9 p.
Protein purifications are often based on the principle of affinity chromatography, where the protein of interest selectively binds to an immobilized ligand. The development of affinity purification requires selecting proper wash and elution conditions. In recent years, miniaturization of the purification process is applied to speed up the development (e.g., microtiterplates, robocolumns). The application of surface plasmon resonance imaging (SPRi) as a tool to simultaneously screen many buffer conditions for wash and elution steps in an affinity-based purification process is studied. Additionally, the protein A ligand stability after exposure to harsh cleaning conditions often limits the reuse of resins and is determined at lab scale. The SPRi technology to screen ligand life-time with respect to alkali stability is used. It is also demonstrated that SPRi can successfully be applied in screening experiments for process developments in a miniaturized approach. The amount of resin, protein and buffer in these studies is reduced 30–300-fold compared to 1 mL column scale, and approximately 10–1000-fold compared to filter plate experiments. The overall development time can be decreased from several months towards days. The multiplexed SPRi can be applied in screening affinity chromatography conditions in early stage development for ligand development and recombinant protein production
Guidelines for Innovation Platforms in Agricultural Research for Development : Decision support for research, development and funding agencies on how to design, budget and implement impactful Innovation Platforms
Schut, M. ; Andersson, J.A. ; Dror, I. ; Kamanda, J. ; Sartas, M. ; Mur, R. ; Kassam, S. ; Brouwer, J.H. ; Stoian, D. ; Devaux, A. ; Velasco, C. ; Gramzow, A. ; Dubois, T. ; Flor, R.J. ; Gummert, M. ; Buizer, Djuna ; McDougall, C. ; Davis, K. ; Homann-Kee Tui, S. ; Lundy, M. - \ 2017
International Institute of Tropical Agriculture - 88 p.
Innovation Platforms are fast becoming part of the mantra of agricultural research for development projects and programmes. Their basic tenet is that stakeholders depend on one another to achieve agricultural development outcomes, and hence need a space where they can learn, negotiate, and coordinate to overcome challenges and capture opportunities through a facilitated innovation process. This important publication provides a critical analysis of Innovation Platforms, their defining features, key functions, and what they can and – as importantly – cannot do.

It will be invaluable reading both for those who fund development projects and
programmes and would like to understand when Innovation Platforms are the approach of choice, and for those practitioners who implement and facilitate Innovation Platforms and would like to understand better their design principles and practical implementation issues.

Because Innovation Platforms have been successful in addressing agricultural challenges, there is a risk that they will be promoted as a panacea for all problems in the agricultural sector. As the authors make clear, however, not all constraints will require Innovation Platforms and, if there is a simpler and cheaper alternative, that should be the first choice. It is essential to think more critically about when, how, and in what form Innovation Platforms can contribute meaningfully to Agricultural development impacts.

The document was developed through a learning collaboration between CGIAR
research centres and other academic and more applied research centres. Eleven
of the 15 CGIAR centres participated and contributed their expertise and experiences across multiple agricultural systems, geographies, and types of complex constraint. The booklet provides information grounded in a rich practical experience of key design and implementation principles, and the financial and human resources that need to be made available, and it makes suggestions for more effective monitoring, evaluation, and learning. It also lists reference materials, answers frequently asked questions, and provides a decision support tool for research, development, and funding agencies.

All in all, this publication offers a lot for those who aspire to make sensible use of
Innovation Platforms in pursuing agricultural development!
Type I interferon is required for T helper (Th) 2 induction by dendritic cells
Webb, Lauren M. ; Lundie, Rachel J. ; Borger, Jessica G. ; Brown, Sheila L. ; Connor, Lisa M. ; Cartwright, Adam N.R. ; Dougall, Annette M. ; Wilbers, Ruud H.P. ; Cook, Peter C. ; Jackson-Jones, Lucy H. ; Phythian-Adams, Alexander T. ; Johansson, Cecilia ; Davis, Daniel M. ; Dewals, Benjamin G. ; Ronchese, Franca ; Macdonald, Andrew S. - \ 2017
The EMBO Journal 36 (2017)16. - ISSN 0261-4189 - p. 2311 - 2465.
Dendritic cell - Interferon - Priming - Th2
Type 2 inflammation is a defining feature of infection with parasitic worms (helminths), as well as being responsible for widespread suffering in allergies. However, the precise mechanisms involved in T helper (Th) 2 polarization by dendritic cells (DCs) are currently unclear. We have identified a previously unrecognized role for type I IFN (IFN-I) in enabling this process. An IFN-I signature was evident in DCs responding to the helminth Schistosoma mansoni or the allergen house dust mite (HDM). Further, IFN-I signaling was required for optimal DC phenotypic activation in response to helminth antigen (Ag), and efficient migration to, and localization with, T cells in the draining lymph node (dLN). Importantly, DCs generated from Ifnar1-/- mice were incapable of initiating Th2 responses in vivo. These data demonstrate for the first time that the influence of IFN-I is not limited to antiviral or bacterial settings but also has a central role to play in DC initiation of Th2 responses.
Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa
Verma, S. ; Bassil, N.V. ; Weg, E. van de; Harrison, R.J. ; Monfort, A. ; Hidalgo, J.M. ; Amaya, I. ; Denoyes, B. ; Mahoney, L.L. ; Davis, T.M. ; Fan, Z. ; Knapp, S. ; Whitaker, V.M. - \ 2017
In: 8th International Strawberry Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611528 - p. 75 - 81.
Breeding - Genotyping - IStraw90 - Single nucleotide polymorphism (SNP)

The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($ 80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of $ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.

Citizen Science Terminology Matters: Exploring Key Terms
Eitzel, M.V. ; Cappadonna, Jessica L. ; Santos-Lang, Chris ; Duerr, Ruth Ellen ; Virapongse, Arika ; West, Sarah Elizabeth ; Kyba, Christopher Conrad Maximillian ; Bowser, Anne ; Cooper, Caren Beth ; Sforzi, Andrea ; Metcalfe, Anya Nova ; Harris, Edward S. ; Thiel, Martin ; Haklay, Mordechai ; Ponciano, Lesandro ; Roche, Joseph ; Ceccaroni, Luigi ; Shilling, Fraser Mark ; Dörler, Daniel ; Heigl, Florian ; Kiessling, Tim ; Davis, Brittany Y. ; Jiang, Qijun - \ 2017
Citizen Science: Theory and Practice 2 (2017)1. - ISSN 2057-4991 - 20 p.
Much can be at stake depending on the choice of words used to describe citizen science, because terminology impacts how knowledge is developed. Citizen science is a quickly evolving field that is mobilizing people’s involvement in information development, social action and justice, and large-scale information gathering. Currently, a wide variety of terms and expressions are being used to refer to the concept of ‘citizen science’ and its practitioners. Here, we explore these terms to help provide guidance for the future growth of this field. We do this by reviewing the theoretical, historical, geopolitical, and disciplinary context of citizen science terminology; discussing what citizen science is and reviewing related terms; and providing a collection of potential terms and definitions for ‘citizen science’ and people participating in citizen science projects. This collection of terms was generated primarily from the broad knowledge base and on-the-ground experience of the authors, by recognizing the potential issues associated with various terms. While our examples may not be systematic or exhaustive, they are intended to be suggestive and invitational of future consideration. In our collective experience with citizen science projects, no single term is appropriate for all contexts. In a given citizen science project, we suggest that terms should be chosen carefully and their usage explained; direct communication with participants about how terminology affects them and what they would prefer to be called also should occur. We further recommend that a more systematic study of terminology trends in citizen science be conducted.
Improved ruminant genetics: Implementation guidance for policymakers and investors
Haas, Y. de; Davis, S. ; Reisinger, A. ; Richards, M. ; Difford, Gareth ; Lassen, Jan - \ 2016
Genetics makes use of natural variation among animals. Selecting preferred animals as parents can yield permanent and cumulative improvements in the population. More efficient animals can greatly reduce greenhouse gas emissions and feed costs. Breeding, including cross-breeding between indigenous and imported species, can also improve resilience to diseases and heat stress and increase reproductive performance.
You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution
Berke, Lidija ; Grandont, Laurie ; Aflitos, S.A. ; Bachem, C.W.B. ; Becker, F.F.M. ; Bouwmeester, K. ; Geest, H.C. van de; Govers, F. ; Jong, Hans de; Peters, S.A. ; Sanchez Perez, G.F. ; Schijlen, E.G.W.M. ; Berg, Ronald van den; Schranz, M.E. - \ 2016
To elucidate the evolutionary history and basis of chromosomal, molecular and phenotypic differences between tomato and potato, genomic data from a key outgroup species is needed. Solanum etuberosum, a non-tuber-bearing species from Chile, fulfills this requirement: its ancestors diverged from the tomato-potato lineage shortly before the split of the tomato and potato clades. With the aim of investigating both genome and trait evolution, we sequenced and assembled the genome of S. etuberosum. The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb and captured 94% of the predicted 702 Mb genome size. The assembly was further scaffolded using
BioNano genome mapping, yielding a final genome assembly that surpassed an N50 of 5Mb.Hence, it is one of the most contiguous Solanum genome assemblies thus far, and with 97% coverage of the expected gene space, also one of the most complete ones. We subsequently annotated the genome
sequence and reconstructed the evolution of genes crucial to potato and/or tomato phenotypes and specifically related to tuber formation, pathogen resistance, flower color and glycoalkaloid biosynthesis. The genome of S. etuberosum thus proved to be an invaluable resource for novel insights in the Solanum genus.
Phytophthora blight in potato: tipping the balance between resistance and susceptibility
Govers, F. ; Wang, Y. ; Du, Y. ; Yang, Shuqing ; Bouwmeester, K. - \ 2016
Plants are continuously challenged by pathogens but because of their effective multi-layered defence system plant diseases are an exception rather than a rule. The first layer of defence is governed by plasma membrane-associated receptors known as pattern recognition receptors (PPRs). The second layer is mediated by intracellular receptors, which are largely nucleotide-binding leucine-rich repeat (NLR) proteins also known as resistance (R) proteins. Our research focuses on late blight, a devastating disease on potato and tomato that is caused by the oomycete pathogen Phytophthora infestans, and infamous because of the Irish potato famine in the mid 19th century. To colonize host plants, pathogens secrete effectors that can modulate host defence. Well-known are the RXLR effectors that are produced by Phytophthora species and related oomycetes, and translocated into host cells. To counteract the pathogen, potato exploits R proteins, the intracellular NLR immune receptors that confer
resistance to P. infestans upon recognition of a RXLR effector, with each R protein having its own matching RXLR effector (or AVR protein). In the absence of a matching R protein, RXLR effectors manipulate the cell machinery by targeting host proteins, the so-called effector targets, thereby paving
the way for successful infection. As an example I will elaborate on the NLR R1 in potato, its matching effector AVR1 in P. infestans, and the AVR1 effector target Sec5, a subunit of the exocyst complex. In addition to R proteins there are also some PRRs known that confer resistance to Phytophthora. We identified a family of cell surface receptors classified as L-type lectin receptor kinases (LecRKs).
Arabidopsis has 45 LecRK genes, of which several play a role in resistance to a variety of plant pathogens including Phytophthora. LecRKs are wide-spread in plants, and this justifies exploitation of LecRKs as novel sources for disease resistance. A further understanding of the mechanisms underlying R protein- and PPR-mediated resistance is crucial to design novel strategies for introducing resistance traits in crops.
Acceleration of ripening-related host cell wall disassembly during Botrytis cinerea infections of unripe tomato fruit
Blanco Ulate, Barbara ; Cantu, D. ; Vincenti, E. ; Kan, J.A.L. van; Hahn, M. ; Labavitch, J.M. ; Powell, A.L.T. - \ 2016
The ripening of tomato fruit is an example of a developmental transition that coincides with increased susceptibility to necrotrophic pathogens, such as Botrytis cinerea. Ripening processes that promote susceptibility include softening-associated disassembly of the fruit host cell wall polysaccharide
networks, modulation of the fruit’s synthesis and perception of plant hormones, accumulation of organic acids and losses of preformed or induced defense responses. As an opportunistic pathogen, B. cinerea modifies its infection strategy to take into account the ripening stage of the host. The diverse and versatile infection mechanisms that B. cinerea deploys on fruit help to define processes that the pathogen may use to hasten fruit susceptibility but also demonstrate that B. cinerea takes advantage of opportune ripening events that render its host vulnerable to aggressive infections. B. cinerea utilizes a large repertoire of enzymes that degrade multiple components of the cell walls of
unripe tomato fruit. However, fruit susceptibility to B. cinerea not only depends on the array of enzymes secreted by the pathogen during infection, but also on modifications that alter the fruit cell wall as part of ripening. We have determined that B. cinerea induces the expression of tomato genes
coding for cell wall degrading proteins that enhance the deconstruction and softening of the fruit tissues. Tomato and B. cinerea genes coding for pectin degrading enzymes are expressed more in infected unripe fruit than in infected ripe fruit. Glycome profiling of cell walls from B. cinerea-infected
and healthy tomato fruit identified changes in the composition and structure of the wall caused by infections that are associated with fungal infections and the normal ripening process. Specific classes of cell wall polysaccharides that are depolymerized by B. cinerea during tomato fruit infections include
the backbones and side-chains of homoglacturonan pectins. We detected significant correlations between the modifications in the fruit cell walls that occurred during B. cinerea infections of unripe fruit and those that occurred as a result of uninfected fruit ripening. Fruit susceptibility assays using B. cinerea knockout mutants of pectin degrading enzymes validated the role of particular enzymes during interactions between tomato fruit and B. cinerea.
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