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.

    We have a manual that explains all the features 

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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.
Drivers of existing and emerging food safety risks : Expert opinion regarding multiple impacts
Kendall, Helen ; Kaptan, Gulbanu ; Stewart, Gavin ; Grainger, Matthew ; Kuznesof, Sharron ; Naughton, Paul ; Clark, Beth ; Hubbard, Carmen ; Raley, Marian ; Marvin, Hans J.P. ; Frewer, Lynn J. - \ 2018
Food Control 90 (2018). - ISSN 0956-7135 - p. 440 - 458.
Delphi technique - Emerging risk - Existing risk - Expert opinion - Food safety
Considerable research effort is invested in the development of evidence to help policy makers and industry deal with the challenges associated with existing and emerging food safety threats. This research aimed to elicit expert views regarding the relationship between the drivers of existing and emerging food safety risks, in order to facilitate their control and mitigation, and to provide the basis for further international policy integration. A Delphi approach involving repeated polling of n = 106 global food safety experts was adopted. The primary drivers of existing and emerging food safety risks were identified to be demographic change, economic driving forces, resource shortages, environmental driving forces, increased complexity of the food supply chain, water security and malevolent activities. The identification of socio-economic and biophysical drivers emphasises the need for a transdisciplinary and systems approach to food safety management and mitigation. The mitigation of hazards on a case-by-case basis is unlikely to have a major impact on food safety hazards but may have unintended effects (where positive or negative) across a broad spectrum of food safety issues. Rather a holistic or systems approach is required which can address both the intended and unintended effects of different drivers and their interactions.
Landscape Architectural Design as Scientific Inquiry?
Lenzholzer, S. - \ 2011
This presentation discusses ‘landscape architectural design as scientific inquiry’ and exemplifies this with the description of a design process within climate-responsive design leading to new design knowledge. ‘Research and design’ are issues that need increasing attention within landscape architecture academia. Substantial contributions on ‘research’ and ‘design’ exist within architectural theory [1,2,3,4]. However, within landscape architecture, there are only few publications on this topic. In those publications, either the definition of ‘research’ was not clearly stated [5] or from the onset, design was not considered to be research “by definition” [6]. This is in contrast to several assertions within architectural theory where design is considered as scientific research. So the question remains: can landscape architectural design also be scientific research? Here, it is stated that design can be scientific research when the design method is similar to a ‘scientific’ method and the aim of the design process is the generation of new knowledge. This requires that research questions are clearly formulated and a systematic, transparent and reliable method of looking for answers is guaranteed. Since there are various ways of conducting scientific research, consequently some ways of ‘design as scientific research’ can be thought of. For instance, ‘design as scientific inquiry’ can mean that design is done similar to action research- as a communicative process from which new knowledge can be gained [7]. But it can also mean that design processes are conducted similar to the methods in the classical empirical sciences. In this presentation, the focus will be on this latter method. In the empirical sciences, normally the research process consists of formulating hypotheses, testing these hypotheses in experiments and generating new knowledge from that. To guarantee reliability, the results are controlled through peer- review. When design is considered an inquiry similar to empirical sciences, possible design solutions are treated as hypotheses and then tested. Zeisel and other authors [8,9,10] proposed this earlier, but they were not clear about the ways design can be tested. Yet, the reliability of testing design is crucial for ‘design as scientific inquiry’. Actually, nowadays modern computer simulation methods offer new avenues for testing designs. With such simulations, the expected effect of design can be tested for many different issues and they can be used within a ‘design as scientific inquiry’ to generate new knowledge. Design processes to generate new knowledge that use these techniques are also widely found within engineering research and development. In this presentation, a similar ‘design as scientific inquiry’ process will be illustrated by an example- a process of climate responsive design to generate new design guidelines for microclimate responsive design of urban squares. This process consisted of generating various design alternatives- or hypotheses- that were expected to be a potential design guideline. These design alternatives were fit for mid-sized urban squares within a Northwest-European maritime climate context. They were all assumed to improve microclimate in the problematic situations: too windy spring and autumn and very hot summer circumstances. The design alternatives were composed of different configurations of vegetation and other elements like pergolas or wind screens that were expected to bring about microclimate improvement. These alternatives are tested with microclimate simulations and the alternative that shows the best effects can be considered as new design knowledge. This design process which had great similarity with scientific research processes can be considered an example for ‘landscape architectural design as scientific research’. [1] Lang. J. 1987. Creating architectural theory, Van Nostrand Reinhold Company, New York [2] Cross, N. 2007. Designerly ways of knowing, Springer, London [3] Laurel, Brenda, ed., 2003, Design Research: Methods and Perspectives. Cambridge: MIT Press [4] de Jong, T.M. and Van der Voordt, D.J.M., 2002, Ways to study and research urban, architectural and technical design, Delft University Press, Delft [5] Milburn, L.S. Brown, Mulley, S.J., Hilts, Steward G., 2003, Assessing academic contributions in landscape architecture, Landscape and Urban Planning 64: 119-129 [6] Milburn, L.S. and Brown, R.D. 2003, The relationship between research and design in landscape architecture, Landscape and Urban Planning 64: 47-66 [7] De Jonge, J.M. (2009) Landscape Architecture between Politics and Science. PhD dissertation, Wageningen University. Blauwdruk, Wageningen [8 ] Zeisel, J. 2006, Inquiry by design (revised edition) W.W. Norton & Company, New York [9] Cross, N., Naughton, J., Walker, D. 1981. Design method and scientific method, Design Studies vol 2 no. 4 pp. 195-201 [10] de Jong, T.M and van der Voordt, D.J.M. 2002 Criteria for scientific study and design, in: de Jong, T.M. and Van der Voordt, D.J.M. (eds.), Ways to study and research urban, architectural and technical design, Delft University Press, Delft, p. 19-30
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