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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    Raptor conservation priorities must incorporate evolution, ecology, and economics, in addition to island endemism
    McClure, Christopher J.W. ; Westrip, James R.S. ; Johnson, Jeff A. ; Schulwitz, Sarah E. ; Virani, Munir Z. ; Davies, Robert ; Symes, Andrew ; Wheatley, Hannah ; Thorstrom, Russell ; Amar, Arjun ; Buij, Ralph ; Jones, Victoria R. ; Williams, Nick P. ; Buechley, Evan R. ; Butchart, Stuart H.M. - \ 2020
    Biological Conservation 245 (2020). - ISSN 0006-3207
    How can decision support tools help reduce nitrate and pesticide pollution from agriculture? A literature review and practical insights from the EU FAIRWAY project
    Nicholson, Fiona ; Laursen, Rikke Krogshave ; Cassidy, Rachel ; Farrow, Luke ; Tendler, Linda ; Williams, John ; Surdyk, Nicolas ; Velthof, Gerard - \ 2020
    Water 12 (2020)3. - ISSN 2073-4441
    Catchment management - Diffuse pollution - Drinking water - DST - Farm advisors - Farm management - Model - Software

    The FAIRWAY project reviewed approaches for protecting drinking water from nitrate and pesticide pollution. A comprehensive assessment of decision support tools (DSTs) used by farmers, advisors, water managers and policy makers across the European Union as an aid to meeting CAP objectives and targets was undertaken, encompassing paper-based guidelines, farm-level and catchment level software, and complex research models. More than 150 DSTs were identified, with 36 ranked for further investigation based on how widely they were used and/or their potential relevance to the FAIRWAY case studies. Of those, most were farm management tools promoting smart nutrient/pesticide use, with only three explicitly considering the impact of mitigation methods on water quality. Following demonstration and evaluation, 12 DSTs were selected for practical testing at nine diverse case study sites, based on their pertinence to local challenges and scales of interest. Barriers to DST exchange between member states were identified and information was collected about user requirements and attitudes. Key obstacles to exchange include differences in legislation, advisory frameworks, country-specific data and calibration requirements, geo-climate and issues around language. Notably, DSTs from different countries using the same input data sometimes delivered very different results. Whilst many countries have developed DSTs to address similar problems, all case study participants were able to draw inspiration from elsewhere. The support and advice provided by skilled advisors was highly valued, empowering end users to most effectively use DST outputs.

    Cereal dietary fibres influence retention time of digesta solid and liquid phases along the gastrointestinal tract
    Low, Dorrain Y. ; Pluschke, Anton M. ; Gerrits, Walter J.J. ; Zhang, Dagong ; Shelat, Kinnari J. ; Gidley, Michael J. ; Williams, Barbara A. - \ 2020
    Food Hydrocolloids 104 (2020). - ISSN 0268-005X
    Arabinoxylan - Digesta - Liquid phase - Retention time - Solid phase - β-glucan

    Nutrient digestion kinetics are determined by gastric emptying (GE) in the stomach and apparent mean retention time (aMRT) along the small and large intestine. This study aimed to evaluate the effects of cereal dietary fibres (DF), either as intrinsic components of plant foods or added ingredients, on the retention of solid and liquid phases of digesta along the gastrointestinal (GI) tract. Thirty pigs were fed one of five diets containing whole wheat (WW), wheat starch (WS) or wheat starch partially replaced by wheat arabinoxylan (AX) or oat β-glucan (βG), or in combination (WSAXβG). Indigestible solid and liquid phase markers were added to each diet and fed at i) constant and ii) pulse dose intervals. Constant markers (acid insoluble ash and chromium) provided aMRT along 11 sections of the GI tract, while pulse dose markers (cerium, ytterbium and cobalt), fed 2–6 h before anaesthesia, provided a GE time. aMRT was slowest in the caecum and large intestine (LI, 15.4h), followed by the small intestine (SI, 3.4h) and stomach (2.6h) with liquid phases moving faster compared to solid phases. Between DF, AX but not βG, delayed GE of solid and liquid contents and showed longer retention time in SI and LI. In the absence of isolated soluble fibres, WS and WW diets showed similar flow characteristics of solid and liquid phases. The aMRT was shown to be dependent on the structure and swellability of added DF.

    Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss
    Lewis, William H. ; Lind, Anders E. ; Sendra, Kacper M. ; Onsbring, Henning ; Williams, Tom A. ; Esteban, Genoveva F. ; Hirt, Robert P. ; Ettema, Thijs J.G. ; Embley, T.M. - \ 2020
    Molecular Biology and Evolution 37 (2020)2. - ISSN 0737-4038 - p. 524 - 539.
    anaerobic metabolism - evolution - genomics - hydrogenosomes - microbial eukaryotes - mitochondria

    Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.

    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis
    Smit, Margot ; Mcgregor, Shauni ; Sun, Heng ; Gough, Catherine ; Bågman, Anne-Maarit ; Soyars, Cara L. ; Kroon, Johan T.M. ; Gaudinier, Allison ; Williams, Clara J. ; Yang, Xiyan ; Nimchuk, Zachary L. ; Weijers, Dolf ; Turner, Simon R. ; Brady, Siobhan M. ; Etchells, Peter - \ 2020
    The Plant Cell 32 (2020)2. - ISSN 1040-4651
    Vascular meristems generate the majority of biomass in higher plants. They constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organisation. However, how these functions are specified and integrated is unknown. Here, a putative PXY-mediated transcriptional regulatory network comprised of 690 transcription factor-promoter interactions was mapped. Among these interactions was a feed-forward loop containing transcription factors WUSCHEL HOMEOBOX RELATED 14 (WOX14) and TARGET OF MONOPTEROS 6 (TMO6), which each regulate the expression of a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN 4 (LBD4). PXY signalling in turn regulates the WOX14, TMO6, LBD4 loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a novel mechanism that influences recruitment of cells into the phloem lineage, and defines the role of PXY signalling in this context to the arrangement of vascular tissue.
    Advances and challenges of life cycle assessment (LCA) of greenhouse gas removal technologies to fight climate changes
    Goglio, P. ; Williams, A.G. ; Balta-Ozkan, N. ; Harris, N.R.P. ; Williamson, P. ; Huisingh, D. ; Zhang, Z. ; Tavoni, M. - \ 2020
    Journal of Cleaner Production 244 (2020). - ISSN 0959-6526
    Climate change - Environmental assessment - Greenhouse gas removal technologies - Life cycle assessment - Methodology - Negative emission technologies

    Several greenhouse gas removal technologies (GGRTs), also called negative emissions technologies (NET) have been proposed to help meet the Paris Climate Agreement targets. However, there are many uncertainties in the estimation of their effective greenhouse gas (GHG) removal potentials, caused by their different levels of technological development. Life Cycle Assessment (LCA) has been proposed as one effective methodology to holistically assess the potential of different GGRT removal approaches but no common framework is currently available for benchmarking and policy development. In this article, challenges for LCA are reviewed and discussed together with some alternative approaches for assessment of GGRTs. In particular, GGRTs pose challenges with regards to the functional unit, the system boundary of the LCA assessment, and the timing of emissions. The need to account within LCA of GGRTs for broader implications which involve environmental impacts, economic, social and political drivers is highlighted. A set of recommendations for LCA of GGRTs are proposed for a better assessment of the GGRTs and better accounting of their carbon removal potentials to meet the targets established within the Paris Agreement.

    Cognitive and Affective Predictors of Illinois Residents’ Perceived Risks from Gray Wolves
    Landon, A. ; Jacobs, M.H. ; Miller, C.A. ; Vaske, J.J. ; Williams, B. - \ 2020
    Society & Natural Resources 33 (2020)5. - ISSN 0894-1920 - p. 574 - 593.
    Increasing wolf populations are a concern for wildlife managers inthe Midwestern U.S. Understanding the psychological mechanismsthat contribute to public perceptions of risk will enable developmentof strategies that seek to mitigate these risks, and suggest where outreach efforts may facilitate acceptance of wolves. We examined the psychological factors that influence Illinois residents’ perceived risks from wolves. We hypothesized that individuals’ perceived risks from wolves were a function of their attitudes toward wolves, negative affect toward wolves, and basic beliefs about wildlife. Data were obtained from a survey of the Illinois public (n¼784). Negative affect and attitudes toward wolves were direct predictors of perceived risks. Basic beliefs predicted attitudes and negative affect toward wolves. Negative affect predicted attitudes. Basic beliefs had direct and indirect effects on perceived risks.
    Optimal dairy feed input selection under alternative feeds availability and relative prices
    Alqaisi, Othman ; Moraes, Luis Eduardo ; Ndambi, Oghaiki Asaah ; Williams, Ryan Blake - \ 2019
    Information Processing in Agriculture 6 (2019)4. - ISSN 2214-3173 - p. 438 - 453.
    Diet formulation - Feed availability - Feed prices - Feed switch - LP modelling

    Feed formulation is essential in the dairy production chain from economic, nutritional, and environmental perspectives. Optimizing the feed formulation across those three domains – given uncertainty of input prices, input availability, and regional climatic conditions – is a challenge for those in the industry. The diet formulation method that is widely used by trading firms and feed production facilities employs a static linear programming (LP) approach. This approach does not allow for intertemporal feed formulations and switches between dietary feed commodities under feed availability conditions, which result in foregone economic gains for feed producers. The current study develops a multi-period LP feed model that uses historical data to capture ration switch opportunities between available feed resources for dairy cows and demonstrates the potential use of the method in different commodity feed availability situations. We apply 14 diet formulations, each covering 150 months, representing a total of 2100 diets. The diet formulation considers a specific milk production level for a “model cow”, alternative feed formulations available, and volatility in feed prices. The results demonstrate that there is an opportunity for efficiency gains in the dairy industry with respect to feed formulation. Based on dietary feed inclusion and price spreads, barley can be an important dairy feed grain which completely replaces wheat, corn, and sorghum at price spreads of less than 94%, less than 78%, and less than 67%, respectively. Grain-based feed scenarios represent the lowest nutrient variation while multiple meal feeds had the lowest costs. Furthermore, and on average, multiple meal feed scenarios provided 10% higher dietary crude protein contents compared to grain based feed scenarios (i.e. 163 vs 179 g/kg DM formulated feed). Meanwhile, multiple meal feeding cost was 11% lower than that in the grain based feeding scenarios. Additionally, the use of multiple meals reduces alfalfa dietary inclusion by 7% on dry matter basis. Our analysis shows a strong reduction in feed cost associated with dietary crude protein reduction equivalent to 7.6 USD/tonne per 1% reduction in dietary crude protein level. The modeling approach allows for the interaction between feed components over time taking into consideration volatile global feed prices, thereby improving feed availability and feed formulation. Overall, the model provides a decision making tool to improve the use of feed resources in the dairy sector.

    Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
    Laine, Veronika N. ; Verhagen, Irene ; Mateman, A.C. ; Pijl, Agata ; Williams, Tony D. ; Gienapp, Phillip ; Oers, Kees van; Visser, Marcel E. - \ 2019
    BMC Genomics 20 (2019). - ISSN 1471-2164
    Aves - Seasonal timing - Selection line - Transcriptomics

    Background: Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression. Results: Birds from the selection lines differed in expression especially for one gene with clear reproductive functions, zona pellucida glycoprotein 4 (ZP4), which has also been shown to be under selection in these lines. Genes were differentially expressed at different time points in all tissues and most of the differentially expressed genes between the two temperature treatments were found in the liver. We identified a set of hub genes from all the tissues which showed high association to hormonal functions, suggesting that they have a core function in timing of breeding. We also found ample differentially expressed genes with largely unknown functions in birds. Conclusions: We found differentially expressed genes associated with selection line and temperature treatment. Interestingly, the latter mainly in the liver suggesting that temperature effects on egg-laying date may happen down-stream in the physiological pathway. These findings, as well as our datasets, will further the knowledge of the mechanisms of tissue-specific avian seasonality in the future.

    Fine-tuning of seasonal timing of breeding is regulated downstream in the underlying neuro-endocrine system in a small songbird
    Verhagen, Irene ; Laine, Veronika N. ; Mateman, A.C. ; Pijl, Agata ; Wit, Ruben de; Lith, Bart van; Kamphuis, Willem ; Viitaniemi, Heidi M. ; Williams, Tony D. ; Caro, Samuel P. ; Meddle, Simone L. ; Gienapp, Phillip ; Oers, Kees van; Visser, Marcel E. - \ 2019
    Journal of Experimental Biology 222 (2019)17. - ISSN 0022-0949
    Gene expression - Individual variation - Parus major - QPCR - Reproductive timing

    The timing of breeding is under selection in wild populations as a result of climate change, and understanding the underlying physiological processes mediating this timing provides insight into the potential rate of adaptation. Current knowledge on this variation in physiology is, however, mostly limited to males. We assessed whether individual differences in the timing of breeding in females are reflected in differences in candidate gene expression and, if so, whether these differences occur in the upstream (hypothalamus) or downstream (ovary and liver) parts of the neuroendocrine system. We used 72 female great tits from two generations of lines artificially selected for early and late egg laying, which were housed in climate-controlled aviaries and went through two breeding cycles within 1 year. In the first breeding season we obtained individual egg-laying dates, while in the second breeding season, using the same individuals, we sampled several tissues at three time points based on the timing of the first breeding attempt. For each tissue, mRNA expression levels were measured using qPCR for a set of candidate genes associated with the timing of reproduction and subsequently analysed for differences between generations, time points and individual timing of breeding. We found differences in gene expression between generations in all tissues, with the most pronounced differences in the hypothalamus. Differences between time points, and early- and late-laying females, were found exclusively in the ovary and liver. Altogether, we show that fine-tuning of the seasonal timing of breeding, and thereby the opportunity for adaptation in the neuroendocrine system, is regulated mostly downstream in the neuro-endocrine system.

    The SF6-technique is a feasible method to estimate the methane emissions from sheep in Norway
    Lind, Vibeke ; Jud, Aurelia ; Ozkan-Gulzari, Seyda ; Richard O Williams, S. - \ 2019
    Harnessing type I CRISPR–Cas systems for genome engineering in human cells
    Cameron, Peter ; Coons, Mary M. ; Klompe, Sanne E. ; Lied, Alexandra M. ; Smith, Stephen C. ; Vidal, Bastien ; Donohoue, Paul D. ; Rotstein, Tomer ; Kohrs, Bryan W. ; Nyer, David B. ; Kennedy, Rachel ; Banh, Lynda M. ; Williams, Carolyn ; Toh, Mckenzi S. ; Irby, Matthew J. ; Edwards, Leslie S. ; Lin, Chun Han ; Owen, Arthur L.G. ; Künne, Tim ; Oost, John van der; Brouns, Stan J.J. ; Slorach, Euan M. ; Fuller, Chris K. ; Gradia, Scott ; Kanner, Steven B. ; May, Andrew P. ; Sternberg, Samuel H. - \ 2019
    Nature Biotechnology 37 (2019). - ISSN 1087-0156 - p. 1471 - 1477.

    Type I CRISPR–Cas systems are the most abundant adaptive immune systems in bacteria and archaea1,2. Target interference relies on a multi-subunit, RNA-guided complex called Cascade3,4, which recruits a trans-acting helicase-nuclease, Cas3, for target degradation5–7. Type I systems have rarely been used for eukaryotic genome engineering applications owing to the relative difficulty of heterologous expression of the multicomponent Cascade complex. Here, we fuse Cascade to the dimerization-dependent, non-specific FokI nuclease domain8–11 and achieve RNA-guided gene editing in multiple human cell lines with high specificity and efficiencies of up to ~50%. FokI–Cascade can be reconstituted via an optimized two-component expression system encoding the CRISPR-associated (Cas) proteins on a single polycistronic vector and the guide RNA (gRNA) on a separate plasmid. Expression of the full Cascade–Cas3 complex in human cells resulted in targeted deletions of up to ~200 kb in length. Our work demonstrates that highly abundant, previously untapped type I CRISPR–Cas systems can be harnessed for genome engineering applications in eukaryotic cells.

    Soft dendritic microparticles with unusual adhesion and structuring properties
    Roh, Sangchul ; Williams, Austin H. ; Bang, Rachel S. ; Stoyanov, Simeon D. ; Velev, Orlin D. - \ 2019
    Nature Materials 18 (2019). - ISSN 1476-1122 - p. 1315 - 1320.

    The interplay between morphology, excluded volume and adhesivity of particles critically determines the physical properties of numerous soft materials and coatings1–6. Branched particles2 or nanofibres3, nanofibrillated cellulose4 or fumed silica5 can enhance the structure-building abilities of colloids, whose adhesion may also be increased by capillarity or binding agents6. Nonetheless, alternative mechanisms of strong adhesion found in nature involve fibrillar mats with numerous subcontacts (contact splitting)7–11 as seen in the feet of gecko lizards and spider webs12–17. Here, we describe the fabrication of hierarchically structured polymeric microparticles having branched nanofibre coronas with a dendritic morphology. Polymer precipitation in highly turbulent flow results in microparticles with fractal branching and nanofibrillar contact splitting that exhibit gelation at very low volume fractions, strong interparticle adhesion and binding into coatings and non-woven sheets. These soft dendritic particles also have potential advantages for food, personal care or pharmaceutical product formulations.

    The landscape of soil carbon data: Emerging questions, synergies and databases
    Malhotra, Avni ; Todd-Brown, Katherine ; Nave, Lucas E. ; Batjes, Niels H. ; Holmquist, James R. ; Hoyt, Alison M. ; Iversen, Colleen M. ; Jackson, Robert B. ; Lajtha, Kate ; Lawrence, Corey ; Vindušková, Olga ; Wieder, William ; Williams, Mathew ; Hugelius, Gustaf ; Harden, Jennifer - \ 2019
    Progress in Physical Geography 43 (2019)5. - ISSN 0309-1333 - p. 707 - 719.
    long-term ecological research - model–data integration - root traits - Soil carbon data - soil carbon stabilization - soil chronosequence - soil database - soil radiocarbon - wetland carbon

    Soil carbon has been measured for over a century in applications ranging from understanding biogeochemical processes in natural ecosystems to quantifying the productivity and health of managed systems. Consolidating diverse soil carbon datasets is increasingly important to maximize their value, particularly with growing anthropogenic and climate change pressures. In this progress report, we describe recent advances in soil carbon data led by the International Soil Carbon Network and other networks. We highlight priority areas of research requiring soil carbon data, including (a) quantifying boreal, arctic and wetland carbon stocks, (b) understanding the timescales of soil carbon persistence using radiocarbon and chronosequence studies, (c) synthesizing long-term and experimental data to inform carbon stock vulnerability to global change, (d) quantifying root influences on soil carbon and (e) identifying gaps in model–data integration. We also describe the landscape of soil datasets currently available, highlighting their strengths, weaknesses and synergies. Now more than ever, integrated soil data are needed to inform climate mitigation, land management and agricultural practices. This report will aid new data users in navigating various soil databases and encourage scientists to make their measurements publicly available and to join forces to find soil-related solutions.

    Spot on: managing Panama disease of banana in the Philippines
    Salacinas, Maricar - \ 2019
    Wageningen University. Promotor(en): G.H.J. Kema, co-promotor(en): H.J.G. Meijer. - Wageningen : Wageningen University - ISBN 9789463325400 - 179

    Banana either cooking or dessert type is regarded as one of the most important crops being staple food or cash crop. Currently the global banana production is threatened by a destructive soil-borne fungus Fusarium odoratissimum colloquially called Tropical race 4 (TR4) causing Panama disease in banana. The on-going dispersal of the pathogen raises the fear of the demise of our beloved banana. As of this writing, there is no concrete solution available to combat the disease, hence manifold of management strategies are explored. With the use of molecular diagnostic tools, this thesis describes the spatial dispersal, epidemiology and management options of Panama disease in the banana belt of the Philippines. This contributes to the development of evidence-based and cost-effective management strategies.

    In the first chapter the subject is presented by unfolding the biology of banana, brief history of its origin, distribution and its cultivation as a staple and cash crop. Having limited genetic variation, the vulnerability of banana to various diseases is described. Panama disease causing serious devastation in banana is elaborated with emphasis on its disease development, spatial and temporal dispersal, disease diagnostics employed and management strategies explored. Statement of the scope of the thesis and outline of the different chapters concluded this chapter.

    The second chapter describes the development of DNA-based diagnostic tool for TR4. In here, a rapid and highly specific detection assay based on Loop Mediated Isothermal Amplification (LAMP) was developed that is pertinent under laboratory and field conditions. The TR4-specific DNA sequence was obtained by Diversity Arrays Technology sequencing of representative genetic diversity of Foc. The specificity of the assay was tested extensively on both target and nontarget isolates and successfully used to detect TR4 in artificially inoculated and naturally infected Cavendish banana corm and pseudostem in the Philippines. Hence, the developed assay offers a powerful tool for epidemiological study on TR4 and is indispensable for implementing quarantine measures.

    The third chapter uncovers the unknown epidemiological phenomena of TR4 dissemination in the banana belt of the Philippines and validate the efficacy of applied management strategy. In here, the spatial distribution of TR4 across soil profiles cropped with either Cavendish or local banana cultivars reveals that the pathogen is distributed across soil layers of up to 1 m below. The dissemination through contaminated soil and water is presented suggesting the importance of deploying biosecurity measures. In the absence of banana host, the long term survival of TR4 on weeds was confirmed emphasizing the importance of weed management in combating Panama disease. Data supporting the efficacy of field sanitation by burning was presented revealing the inefficiency of the procedure to eliminate TR4 propagule in the soil and should be reconsidered. Together, this findings emphasize the need for an integrated and evidence-based Panama disease management strategies.

    The fourth chapter put emphasis on the efficacy of disinfectants used as front-line defense against TR4 spread in the banana production areas in the Philippines. In this study, disinfectants of different active ingredients, rate and exposure time were tested in vitro against different propagules of TR4 to include mycelia, conidiospores, chlamydospores suspensions and chlamydospores-infested soil. The TR4 mycelia and conidia are sensitive to disinfectants tested at the manufacturer’s recommended concentration. The thick-walled chlamydospores were remarkably sensitive to disinfectants in suspension but the same compounds were largely ineffective against chlamydospores in soil except for diamidine-based disinfectant. Summing up, the rational choice of appropriate disinfectants should be facilitated by reliable data on efficacy under various biological, environmental and temporal conditions, corrosiveness and costs. The utilization of disinfectants should be maximized and properly implemented to stop or slow down TR4 dissemination within and between farms at local, regional or international scale.

    The fifth chapter investigates the potential of anaerobic soil disinfestation (ASD) as a biological option for Panama disease management. In this study, two commercially available organic amendments were tested both under laboratory and field conditions in the naturally infested soils in the Philippines. Controlled condition in the laboratory resulted to reduction of viable TR4 chlamydospores to 0.01% in plastic containers after four weeks treatment supported by the production of toxic gases and volatile fatty acids. The pilot field experimentation displayed a hundred-fold reduction of TR4 chlamydospores level relative to the control after eight weeks field treatment. A significant reduction of Panama disease recurrence was recorded on replanted Cavendish “Williams” banana monitored for one cropping cycle. These promising results might contribute to short-term management options to continue banana production in Panama disease affected farms.

    The last chapter summarizes the findings gathered in this PhD project. The continued local and international TR4 dispersal is discussed in relation to containment strategies and management options currently employed. The importance of the molecular diagnostic tool to chart progression of disease spread is discussed. The systematic approach to manage soil-borne pathogens are reviewed linking to the current practices to continue banana production despite the presence of TR4. The pathogen inoculum density and disease incidence curve was correlated to the current knowledge. This gives rise to the statement that partial resistance to Panama disease does not ultimately contributes to sustainable disease control. The intended long-term perspective for banana growing lies in an integrated management strategy that includes the use of multiple resistant banana varieties.

    Systems genetics for evolutionary studies
    Prins, Pjotr ; Smant, Geert ; Arends, Danny ; Mulligan, Megan K. ; Williams, Rob W. ; Jansen, Ritsert C. - \ 2019
    In: Evolutionary Genomics / Anisimova, Maria, New York : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493990733 - p. 635 - 652.
    eQTL - Evolution - GEMMA - GeneNetwork - Genetical genomics - Genomics - LMM - Metabolomics - Network inference - NGS - QTL - R-genes - R/qtl - Systems genetics - xQTL

    Systems genetics combines high-throughput genomic data with genetic analysis. In this chapter, we review and discuss application of systems genetics in the context of evolutionary studies, in which high-throughput molecular technologies are being combined with quantitative trait locus (QTL) analysis in segregating populations. The recent explosion of high-throughput data—measuring thousands of RNAs, proteins, and metabolites, using deep sequencing, mass spectrometry, chromatin, methyl-DNA immunoprecipitation, etc.—allows the dissection of causes of genetic variation underlying quantitative phenotypes of all types. To deal with the sheer amount of data, powerful statistical tools are needed to analyze multidimensional relationships and to extract valuable information and new modes and mechanisms of changes both within and between species. In the context of evolutionary computational biology, a well-designed experiment and the right population can help dissect complex traits likely to be under selection using proven statistical methods for associating phenotypic variation with chromosomal locations. Recent evolutionary expression QTL (eQTL) studies focus on gene expression adaptations, mapping the gene expression landscape, and, tentatively, define networks of transcripts and proteins that are jointly modulated sets of eQTL networks. Here, we discuss the possibility of introducing an evolutionary “prior” in the form of gene families displaying evidence of positive selection, and using that prior in the context of an eQTL experiment for elucidating host-pathogen protein-protein interactions. Here we review one exemplar evolutionairy eQTL experiment and discuss experimental design, choice of platforms, analysis methods, scope, and interpretation of results. In brief we highlight how eQTL are defined; how they are used to assemble interacting and causally connected networks of RNAs, proteins, and metabolites; and how some QTLs can be efficiently converted to reasonably well-defined sequence variants.

    Assessing the potential of soil carbonation and enhanced weathering through Life Cycle Assessment: A case study for Sao Paulo State, Brazil
    Lefebvre, David ; Goglio, Pietro ; Williams, Adrian ; Manning, David A.C. ; Azevedo, Antonio Carlos de; Bergmann, Magda ; Meersmans, Jeroen ; Smith, Pete - \ 2019
    Journal of Cleaner Production 233 (2019). - ISSN 0959-6526 - p. 468 - 481.
    Carbonation - Enhanced weathering - LCA - Life cycle assessment - NET - Sao paulo

    Enhanced silicate rock weathering for long-term carbon dioxide sequestration has considerable potential, but depends on the availability of suitable rocks coupled with proximity to suitable locations for field application. In this paper, we investigate the established mining industry that extracts basaltic rocks for construction from the Paraná Basin, Sao Paulo State, Brazil. Through a Life Cycle Assessment, we determine the balance of carbon dioxide emissions involved in the use of this material, the relative contribution of soil carbonation and enhanced weathering, and the potential carbon dioxide removal of Sao Paulo agricultural land through enhanced weathering of basalt rock. Our results show that enhanced weathering and carbonation respectively emit around 75 and 135 kg carbon dioxide equivalent per tonne of carbon dioxide equivalent removed (considering a quarry to field distance of 65 km). We underline transportation as the principal process negatively affecting the practice and uncover a limiting road travel distance from the quarry to the field of 540 ± 65 km for carbonation and 990 ± 116 km for enhanced weathering, above which the emissions offset the potential capture. Regarding Sao Paulo State, the application of crushed basalt at 1 t/ha to all of the State's 12 million hectares of agricultural land could capture around 1.3 to 2.4 Mt carbon dioxide equivalent through carbonation and enhanced weathering, respectively. This study suggests a lower sequestration estimate than previous studies and emphasizes the need to consider all process stages through a Life Cycle Assessment methodology, to provide more reliable estimates of the sequestration potential of greenhouse gas removal technologies.

    Loss rates of honey bee colonies during winter 2017/18 in 36 countries participating in the COLOSS survey, including effects of forage sources
    Gray, Alison ; Brodschneider, Robert ; Adjlane, Noureddine ; Ballis, Alexis ; Brusbardis, Valters ; Charrière, Jean Daniel ; Chlebo, Robert ; F. Coffey, Mary ; Cornelissen, Bram ; Amaro da Costa, Cristina ; Csáki, Tamás ; Dahle, Bjørn ; Danihlík, Jiří ; Dražić, Marica Maja ; Evans, Garth ; Fedoriak, Mariia ; Forsythe, Ivan ; Graaf, Dirk de; Gregorc, Aleš ; Johannesen, Jes ; Kauko, Lassi ; Kristiansen, Preben ; Martikkala, Maritta ; Martín-Hernández, Raquel ; Medina-Flores, Carlos Aurelio ; Mutinelli, Franco ; Patalano, Solenn ; Petrov, Plamen ; Raudmets, Aivar ; Ryzhikov, Vladimir A. ; Simon-Delso, Noa ; Stevanovic, Jevrosima ; Topolska, Grazyna ; Uzunov, Aleksandar ; Vejsnaes, Flemming ; Williams, Anthony ; Zammit-Mangion, Marion ; Soroker, Victoria - \ 2019
    Journal of Apicultural Research 58 (2019)4. - ISSN 0021-8839 - p. 479 - 485.
    Apis mellifera - beekeeping - citizen science - colony winter losses - forage sources - monitoring - mortality - survey

    This short article presents loss rates of honey bee colonies over winter 2017/18 from 36 countries, including 33 in Europe, from data collected using the standardized COLOSS questionnaire. The 25,363 beekeepers supplying data passing consistency checks in total wintered 544,879 colonies, and reported 26,379 (4.8%, 95% CI 4.7–5.0%) colonies with unsolvable queen problems, 54,525 (10.0%, 95% CI 9.8–10.2%) dead colonies after winter and another 8,220 colonies (1.5%, 95% CI 1.4–1.6%) lost through natural disaster. This gave an overall loss rate of 16.4% (95% CI 16.1–16.6%) of honey bee colonies during winter 2017/18, but this varied greatly from 2.0 to 32.8% between countries. The included map shows relative risks of winter loss at regional level. The analysis using the total data-set confirmed findings from earlier surveys that smaller beekeeping operations with at most 50 colonies suffer significantly higher losses than larger operations (p <.001). Beekeepers migrating their colonies had significantly lower losses than those not migrating (p <.001), a different finding from previous research. Evaluation of six different forage sources as potential risk factors for colony loss indicated that intensive foraging on any of five of these plant sources (Orchards, Oilseed Rape, Maize, Heather and Autumn Forage Crops) was associated with significantly higher winter losses. This finding requires further study and explanation. A table is included giving detailed results of loss rates and the impact of the tested forage sources for each country and overall.

    Whose Deficit Anyway? Institutional Misunderstanding of Fracking-Sceptical Publics
    Williams, Laurence ; Macnaghten, Philip ; Turnhout, E. ; Tuinstra, W. ; Halffman, Willem - \ 2019
    In: Environmental Expertise Cambridge University Press - ISBN 9781316162514 - p. 90 - 103.
    Hydraulic fracturing, or fracking, is a relatively new technique used to extract oil or natural gas. It is a highly contested technique, with often-fierce disagreements about its safety and environmental impacts between experts, governments, oil companies, and inhabitants. This case focuses on public resistance to fracking, offering a useful illustration of the limitations of the information deficit model (Section 4.4) and showing that controversies cannot be resolved by assuming that opposing actors suffer from an information deficit that can be rectified by means of better communication and greater public understanding of science
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