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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    Aryl hydrocarbon Receptor activation during In vitro and in vivo digestion of raw and cooked broccoli (brassica oleracea var. Italica)
    Koper, Jonna E.B. ; Kortekaas, Maaike ; Loonen, Linda M.P. ; Huang, Zhan ; Wells, Jerry M. ; Gill, Chris I.R. ; Pourshahidi, L.K. ; McDougall, Gordon ; Rowland, Ian ; Pereira-Caro, Gema ; Fogliano, Vincenzo ; Capuano, Edoardo - \ 2020
    Food & Function 11 (2020)5. - ISSN 2042-6496 - p. 4026 - 4037.

    Broccoli is rich in glucosinolates, which can be converted upon chewing and processing into Aryl hydrocarbon Receptor (AhR) ligands. Activation of AhR plays an important role in overall gut homeostasis but the role of broccoli processing on the generation of AhR ligands is still largely unknown. In this study, the effects of temperature, cooking method (steaming versus boiling), gastric pH and further digestion of broccoli on AhR activation were investigated in vitro and in ileostomy subjects. For the in vitro study, raw, steamed (t = 3 min and t = 6 min) and boiled (t = 3 min and t = 6 min) broccoli were digested in vitro with different gastric pH. In the in vivo ileostomy study, 8 subjects received a broccoli soup or a broccoli soup plus an exogenous myrosinase source. AhR activation was measured in both in vitro and in vivo samples by using HepG2-Lucia™ AhR reporter cells. Cooking broccoli reduced the AhR activation measured after gastric digestion in vitro, but no effect of gastric pH was found. Indole AhR ligands were not detected or detected at very low levels both after intestinal in vitro digestion and in the ileostomy patient samples, which resulted in no AhR activation. This suggests that the evaluation of the relevance of glucosinolates for AhR modulation in the gut cannot prescind from the way broccoli is processed, and that broccoli consumption does not necessarily produce substantial amounts of AhR ligands in the large intestine.

    An invitation for more research on transnational corporations and the biosphere
    Folke, Carl ; Österblom, Henrik ; Jouffray, Jean Baptiste ; Lambin, Eric F. ; Adger, Neil ; Scheffer, Marten ; Crona, Beatrice I. ; Nyström, Magnus ; Levin, Simon A. ; Carpenter, Stephen R. ; Anderies, John M. ; Chapin, Stuart ; Crépin, Anne Sophie ; Dauriach, Alice ; Galaz, Victor ; Gordon, Line J. ; Kautsky, Nils ; Walker, Brian H. ; Watson, James R. ; Wilen, James ; Zeeuw, Aart de - \ 2020
    Nature Ecology & Evolution 4 (2020). - ISSN 2397-334X
    Big data in livestock offers great potential to study heritable variation in environmental variance: a case study in dairy cattle
    Mulder, Han A. ; Poppe, H.W.M. ; Berghof, T.V.L. - \ 2019
    Detection of reciprocal translocations using short read sequencing
    Bouwman, A.C. ; Pas, M.F.W. te; Derks, M.F.L. ; Groenen, M. ; Veerkamp, R.F. ; Broekhuijse, Marleen L.W.J. ; Harlizius, Barbara - \ 2019
    Earth System Governance : Science and Implementation Plan of the Earth System Governance Project 2018
    Burch, Sarah ; Gupta, A. ; Yumie Aoki Inoue, Christina ; Kalfagianni, Agni ; Persson, Asa ; Heijden, Jeroen van der; Vervoort, Joost ; Adler, Carolina ; Bloomfield, Michael John ; Djalante, Riyanti ; Dryzek, John S. ; Galaz, Victor ; Gordon, Christopher ; Harmon, Renee ; Jinnah, Sikina ; Kim, Rakhyun E. ; Olsson, Lennart ; Leeuwen, J. van; Ramasar, Vasna ; Wapner, Paul ; Zondervan, Ruben - \ 2019
    Utrecht : Earth System Governance - 128 p.
    Transnational corporations and the challenge of biosphere stewardship
    Folke, Carl ; Österblom, Henrik ; Jouffray, Jean Baptiste ; Lambin, Eric F. ; Adger, W.N. ; Scheffer, Marten ; Crona, Beatrice I. ; Nyström, Magnus ; Levin, Simon A. ; Carpenter, Stephen R. ; Anderies, John M. ; Chapin, Stuart ; Crépin, Anne Sophie ; Dauriach, Alice ; Galaz, Victor ; Gordon, Line J. ; Kautsky, Nils ; Walker, Brian H. ; Watson, James R. ; Wilen, James ; Zeeuw, Aart de - \ 2019
    Nature Ecology & Evolution 3 (2019)10. - ISSN 2397-334X - p. 1396 - 1403.

    Sustainability within planetary boundaries requires concerted action by individuals, governments, civil society and private actors. For the private sector, there is concern that the power exercised by transnational corporations generates, and is even central to, global environmental change. Here, we ask under which conditions transnational corporations could either hinder or promote a global shift towards sustainability. We show that a handful of transnational corporations have become a major force shaping the global intertwined system of people and planet. Transnational corporations in agriculture, forestry, seafood, cement, minerals and fossil energy cause environmental impacts and possess the ability to influence critical functions of the biosphere. We review evidence of current practices and identify six observed features of change towards 'corporate biosphere stewardship', with significant potential for upscaling. Actions by transnational corporations, if combined with effective public policies and improved governmental regulations, could substantially accelerate sustainability efforts.

    The Earth System Governance Project as a network organization: a critical assessment after ten years
    Biermann, F. ; Betsill, Michele M. ; Burch, S. ; Dryzek, John ; Gordon, Christopher ; Gupta, A. ; Gupta, Joyeeta ; Inoue, Cristina ; Kalfagianni, Agni ; Kanie, Norichika ; Olsson, Lennart ; Persson, Åsa ; Schroeder, H. ; Scobie, Michelle - \ 2019
    Current Opinion in Environmental Sustainability 39 (2019). - ISSN 1877-3435 - p. 17 - 23.

    The social sciences have engaged since the late 1980s in international collaborative programmes to study questions of sustainability and global change. This article offers an in-depth analysis of the largest long-standing social-science network in this field: the Earth System Governance Project. Originating as a core project of the former International Human Dimensions Programme on Global Environmental Change, the Earth System Governance Project has matured into a global, self-sustaining research network, with annual conferences, numerous taskforces, research centers, regional research fellow meetings, three book series, an open access flagship journal, and a lively presence in social media. The article critically reviews the experiences of the Earth System Governance network and its integration and interactions with other programmes over the last decade.

    Integration of Quantitative Genetic and Epidemiological Theory and Models of Infectious Diseases
    Bijma, Piter - \ 2019
    Genomic selection: Causing a (r)evolution in the genetic architecture of traits?
    Wientjes, Yvonne - \ 2019
    Poster
    New directions in earth system governance research
    Burch, Sarah ; Gupta, A. ; Inoue, C. ; Kalfagianni, Agni ; Persson, Asa ; Gerlak, Andrea K. ; Ishii, Atsushi ; Patterson, James ; Pickering, Jonathan ; Scobie, M. ; Heijden, Jeroen van der; Vervoort, J. ; Adler, Carolina ; Bloomfield, Michael ; Djalante, Riyante ; Dryzek, John ; Galaz, Victor ; Gordon, Christopher ; Harmon, Renée ; Jinnah, Sikina ; Kim, Rakhyun E. ; Olsson, Lennart ; Leeuwen, J. van; Ramasar, Vasna ; Wapner, Paul ; Zondervan, R. - \ 2019
    Earth System Governance 1 (2019). - ISSN 2589-8116 - 18 p.
    Governance - Research networks - Earth system - Transformation
    The Earth System Governance project is a global research alliance that explores novel, effective governance mechanisms to cope with the current transitions in the biogeochemical systems of the planet. A decade after its inception, this article offers an overview of the project's new research framework (which is built upon a review of existing earth system governance research), the goal of which is to continue to stimulate a pluralistic, vibrant and relevant research community. This framework is composed of contextual conditions (transformations, inequality, Anthropocene and diversity), which capture what is being observed empirically, and five sets of research lenses (architecture and agency, democracy and power, justice and allocation, anticipation and imagination, and adaptiveness and reflexivity). Ultimately the goal is to guide and inspire the systematic study of how societies prepare for accelerated climate change and wider earth system change, as well as policy responses.
    Discovery of Salmonella trehalose phospholipids reveals functional convergence with mycobacteria
    Reinink, Peter ; Buter, Jeffrey ; Mishra, Vivek K. ; Ishikawa, Eri ; Cheng, Tan Yun ; Willemsen, Peter T.J. ; Porwollik, Steffen ; Brennan, Patrick J. ; Heinz, Eva ; Mayfield, Jacob A. ; Dougan, Gordon ; Els, Cécile A. van; Cerundolo, Vincenzo ; Napolitani, Giorgio ; Yamasaki, Sho ; Minnaard, Adriaan J. ; McClelland, Michael ; Moody, D.B. ; Rhijn, Ildiko Van - \ 2019
    Journal of Experimental Medicine 216 (2019)4. - ISSN 0022-1007 - p. 757 - 771.

    Salmonella species are among the world's most prevalent pathogens. Because the cell wall interfaces with the host, we designed a lipidomics approach to reveal pathogen-specific cell wall compounds. Among the molecules differentially expressed between Salmonella Paratyphi and S. Typhi, we focused on lipids that are enriched in S. Typhi, because it causes typhoid fever. We discovered a previously unknown family of trehalose phospholipids, 6,6'-diphosphatidyltrehalose (diPT) and 6-phosphatidyltrehalose (PT). Cardiolipin synthase B (ClsB) is essential for PT and diPT but not for cardiolipin biosynthesis. Chemotyping outperformed clsB homology analysis in evaluating synthesis of diPT. DiPT is restricted to a subset of Gram-negative bacteria: large amounts are produced by S. Typhi, lower amounts by other pathogens, and variable amounts by Escherichia coli strains. DiPT activates Mincle, a macrophage activating receptor that also recognizes mycobacterial cord factor (6,6'-trehalose dimycolate). Thus, Gram-negative bacteria show convergent function with mycobacteria. Overall, we discovered a previously unknown immunostimulant that is selectively expressed among medically important bacterial species.

    Food in the Anthropocene : the EAT–Lancet Commission on healthy diets from sustainable food systems
    Willett, Walter ; Rockström, Johan ; Loken, Brent ; Springmann, Marco ; Lang, Tim ; Vermeulen, Sonja ; Garnett, Tara ; Tilman, David ; DeClerck, Fabrice ; Wood, Amanda ; Jonell, Malin ; Clark, Michael ; Gordon, Line J. ; Fanzo, Jessica ; Hawkes, Corinna ; Zurayk, Rami ; Rivera, Juan A. ; Vries, Wim De; Majele Sibanda, Lindiwe ; Afshin, Ashkan ; Chaudhary, Abhishek ; Herrero, Mario ; Agustina, Rina ; Branca, Francesco ; Lartey, Anna ; Fan, Shenggen ; Crona, Beatrice ; Fox, Elizabeth ; Bignet, Victoria ; Troell, Max ; Lindahl, Therese ; Singh, Sudhvir ; Cornell, Sarah E. ; Srinath Reddy, K. ; Narain, Sunita ; Nishtar, Sania ; Murray, Christopher J.L. - \ 2019
    The Lancet 393 (2019)10170. - ISSN 0140-6736 - p. 447 - 492.
    1. Unhealthy and unsustainably produced food poses a global risk to people and the planet. More than 820 million people have insufficient food and many more consume an unhealthy diet that contributes to premature death and morbidity. Moreover, global food production is the largest pressure caused by humans on Earth, threatening local ecosystems and the stability of the Earth system. 2. Current dietary trends, combined with projected population growth to about 10 billion by 2050, will exacerbate risks to people and planet. The global burden of non-communicable diseases is predicted to worsen and the effects of food production on greenhouse-gas emissions, nitrogen and phosphorus pollution, biodiversity loss, and water and land use will reduce the stability of the Earth system. 3. Transformation to healthy diets from sustainable food systems is necessary to achieve the UN Sustainable Development Goals and the Paris Agreement, and scientific targets for healthy diets and sustainable food production are needed to guide a Great Food Transformation. 4. Healthy diets have an appropriate caloric intake and consist of a diversity of plant-based foods, low amounts of animal source foods, unsaturated rather than saturated fats, and small amounts of refined grains, highly processed foods, and added sugars. 5. Transformation to healthy diets by 2050 will require substantial dietary shifts, including a greater than 50% reduction in global consumption of unhealthy foods, such as red meat and sugar, and a greater than 100% increase in consumption of healthy foods, such as nuts, fruits, vegetables, and legumes. However, the changes needed differ greatly by region. 6. Dietary changes from current diets to healthy diets are likely to substantially benefit human health, averting about 10·8–11·6 million deaths per year, a reduction of 19·0–23·6%. 7. With food production causing major global environmental risks, sustainable food production needs to operate within the safe operating space for food systems at all scales on Earth. Therefore, sustainable food production for about 10 billion people should use no additional land, safeguard existing biodiversity, reduce consumptive water use and manage water responsibly, substantially reduce nitrogen and phosphorus pollution, produce zero carbon dioxide emissions, and cause no further increase in methane and nitrous oxide emissions. 8. Transformation to sustainable food production by 2050 will require at least a 75% reduction of yield gaps, global redistribution of nitrogen and phosphorus fertiliser use, recycling of phosphorus, radical improvements in efficiency of fertiliser and water use, rapid implementation of agricultural mitigation options to reduce greenhouse-gas emissions, adoption of land management practices that shift agriculture from a carbon source to sink, and a fundamental shift in production priorities. 9. The scientific targets for healthy diets from sustainable food systems are intertwined with all UN Sustainable Development Goals. For example, achieving these targets will depend on providing high-quality primary health care that integrates family planning and education on healthy diets. These targets and the Sustainable Development Goals on freshwater, climate, land, oceans, and biodiversity will be achieved through strong commitment to global partnerships and actions. 10. Achieving healthy diets from sustainable food systems for everyone will require substantial shifts towards healthy dietary patterns, large reductions in food losses and waste, and major improvements in food production practices. This universal goal for all humans is within reach but will require adoption of scientific targets by all sectors to stimulate a range of actions from individuals and organisations working in all sectors and at all scales.
    A research roadmap for quantifying non-state and subnational climate mitigation action
    Hsu, Angel ; Höhne, Niklas ; Kuramochi, Takeshi ; Roelfsema, Mark ; Weinfurter, Amy ; Xie, Yihao ; Lütkehermöller, Katharina ; Chan, Sander ; Corfee-Morlot, Jan ; Drost, Philip ; Faria, Pedro ; Gardiner, Ann ; Gordon, David J. ; Hale, Thomas ; Hultman, Nathan E. ; Moorhead, John ; Reuvers, Shirin ; Setzer, Joana ; Singh, Neelam ; Weber, Christopher ; Widerberg, Oscar - \ 2019
    Nature Climate Change 9 (2019)1. - ISSN 1758-678X - p. 11 - 17.

    Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.

    Economics of agricultural biotechnology
    Zilberman, David ; Wesseler, J.H.H. ; Schmitz, Andrew ; Gordon, Ben - \ 2018
    In: The Routledge Handbook of Agricultural Economics / L. Cramer, Gail, P. Paudel, Krishna, Schmitz, Andrew, London : Routledge - ISBN 9781138654235 - p. 670 - 686.
    This chapter surveys the economics of the impact of genetic engineering (GE) in agriculture. Research shows that adoption of these technologies has increased crop yields and farm income, while reducing pesticide, input use, and greenhouse gas emissons from agriculture. The adoption of GE has been impeded by heavy regulatory constraints resulting from political economic considerations. The underutilization of GE in agriculture has negative impacts on ecnomic welfare, especially the poor in developing countries.
    Options for keeping the food system within environmental limits
    Springmann, Marco ; Clark, Michael ; Mason-D’Croz, Daniel ; Wiebe, Keith ; Bodirsky, Benjamin Leon ; Lassaletta, Luis ; Vries, Wim de; Vermeulen, Sonja J. ; Herrero, Mario ; Carlson, Kimberly M. ; Jonell, Malin ; Troell, Max ; DeClerck, Fabrice ; Gordon, Line J. ; Zurayk, Rami ; Scarborough, Peter ; Rayner, Mike ; Loken, Brent ; Fanzo, Jess ; Godfray, H.C.J. ; Tilman, David ; Rockström, Johan ; Willett, Walter - \ 2018
    Nature 562 (2018)7728. - ISSN 0028-0836 - p. 519 - 525.

    The food system is a major driver of climate change, changes in land use, depletion of freshwater resources, and pollution of aquatic and terrestrial ecosystems through excessive nitrogen and phosphorus inputs. Here we show that between 2010 and 2050, as a result of expected changes in population and income levels, the environmental effects of the food system could increase by 50–90% in the absence of technological changes and dedicated mitigation measures, reaching levels that are beyond the planetary boundaries that define a safe operating space for humanity. We analyse several options for reducing the environmental effects of the food system, including dietary changes towards healthier, more plant-based diets, improvements in technologies and management, and reductions in food loss and waste. We find that no single measure is enough to keep these effects within all planetary boundaries simultaneously, and that a synergistic combination of measures will be needed to sufficiently mitigate the projected increase in environmental pressures.

    Using 'omic approaches to compare temporal bacterial colonization of lolium perenne, lotus corniculatus, and trifolium pratensein the Rumen
    Elliott, Christopher L. ; Edwards, Joan E. ; Wilkinson, Toby J. ; Allison, Gordon G. ; McCaffrey, Kayleigh ; Scott, Mark B. ; Rees-Stevens, Pauline ; Kingston-Smith, Alison H. ; Huws, Sharon A. - \ 2018
    Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X - 16 p.
    16S rRNA gene - Birds foot trefoil - CowPI - FTIR - Microbiome - Perennial ryegrass - Red clover - Rumen

    Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

    Opening design and innovation processes in agriculture : Insights from design and management sciences and future directions
    Berthet, Elsa T. ; Hickey, Gordon M. ; Klerkx, Laurens - \ 2018
    Agricultural Systems 165 (2018). - ISSN 0308-521X - p. 111 - 115.
    Actor-network theory - Affordances - Agricultural innovation systems - Bioeconomy - Boundary objects - Circular economy - Co-innovation - Design reasoning - Food systems - Interactive design - Materiality - Network management - Open innovation - Sustainability transitions

    Research has identified an urgent need to renew agriculture's traditional design organization and foster more open, decentralized, contextualized and participatory approaches to design and innovation. While the concepts of co-design and co-innovation used in agriculture resemble features of open innovation, they may benefit from ‘inbound open innovation’ themselves through cross-fertilization with management studies, design science, science and technology studies, and organization studies. This special issue brings together different streams of research providing novel perspectives on co-design and co-innovation in agriculture, including methods, tools and organizations. It compares empirical experiences and theoretical advances to address a variety of issues (e.g., innovation ecosystems, collective design management, participatory design methods, affordances of system analysis tools and network leadership) that shed new light on co-design and co-innovation in support of sustainable agriculture and more broadly transitions towards a diversity of food systems and a circular bioeconomy. This introductory paper presents crosscutting insights and distills from these three directions for future research and practice in agricultural design and innovation: 1) Further opening design and innovation techniques and tools to better account for visual, auditory, tactile and olfactory expressions in evolving designs and what they afford users; 2) Further opening innovation networks in view of creating and stimulating integrative niches that can foster sustainability transitions, which also requires network managers instilling a reflexive stance of network members and broader awareness of power structures attached to organizational, sector and paradigmatic silos in agricultural systems; and 3) Further opening the range of innovation actors to include non-human actants to better account for the agency of the material and ecological.

    Beyond agricultural innovation systems? Exploring an agricultural innovation ecosystems approach for niche design and development in sustainability transitions
    Pigford, Ashlee Ann E. ; Hickey, Gordon M. ; Klerkx, Laurens - \ 2018
    Agricultural Systems 164 (2018). - ISSN 0308-521X - p. 116 - 121.
    Agricultural innovation ecosystems - Change agency - Mission oriented innovation policy - Socio-ecological systems - Sustainability transitions - Sustainable agriculture - Systems design
    Well-designed and supported innovation niches may facilitate transitions towards sustainable agricultural futures, which may follow different approaches and paradigms such as agroecology, local place-based food systems, vertical farming, bioeconomy, urban agriculture, and smart farming or digital farming. In this paper we consider how the existing agricultural innovation systems (AIS) approach might be opened up to better support the creation of innovation niches. We engage with Innovation Ecosystems thinking to consider the ways in which it might enhance efforts to create multi-actor, cross-sectoral innovation niches that are capable of supporting transitions to sustainable agricultural systems across multiple scales. While sharing many similarities with AIS thinking, Innovation Ecosystems thinking has the potential to broaden AIS by: emphasizing the role of power in shaping directionality in innovation platforms or innovation communities that are connected to niches and their interaction with regimes; highlighting the plurality of actors and actants and the integral role of ecological actants in innovation; and offering an umbrella concept through which to cross scalar and paradigmatic or sector boundaries in order to engage with a variety of innovation systems affecting multifunctional agricultural landscapes and systems. To this end, an Agricultural Innovation Ecosystems approach may help design and support development of transboundary, inter-sectoral innovation niches that can realize more collective and integrated innovation in support of sustainability transitions, and help enact mission oriented agricultural innovation policy.
    A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
    Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
    Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
    Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
    Identification of natural variants that influence behavioral responses to ethanol in C. elegans
    Bettinger, Jill ; Kammenga, J.E. ; Mathies, Laura ; Davies, Andrew - \ 2018
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