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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The economics of vegetable farming in the lowlands of Cirebon, West Java, Indonesia
Adiyoga, W. ; Putter, H. de - \ 2018
In: Proceedings of the 2nd Asian Horticultural Congress. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462612051 - p. 297 - 304.
Economics - Farm records - Lowlands - Price risk - Vegetable - Yield risk

The study was aiming at examining the economics of vegetable production of ten farmers in the lowlands of Cirebon, West Java, Indonesia. Farm records that documented the farmers materials and labor and the costs and income of vegetable crops grown from July 2013 to September 2015 were collected. In total, 65 vegetable crop records were collected i.e., bitter gourd (1), hot pepper (1), rice (3), shallot (33), sweet corn (23), spinach (2), and yard long bean (2). Farm-record results show that the farm/firm-base profits range from -37,000 to 506,000 IDR. Referring to the legal minimum wage, it implies that each farm/firm should provide at least 50,000 IDR day-1. This implies that five out of ten farmers/households have incomes lower than the local legal minimum wage. This may also imply that within two years of cultivating vegetables, half of the farmers participating in the farm-record activity frequently experienced a loss. The two most uncertain factors affecting farmers’ income are production (yield) and marketing (price) risks. It is suggested that farmers may forego an enterprise that has a high potential for income but also carries a high risk for loss, and instead choose an enterprise which is less profitable but also less risky. For example, instead of growing shallot 3-4 times in a row, farmers may use sweet corn as a rotation crop. The possible solution for overcoming marketing risks is through developing institutional arrangements, such as collective marketing or contract farming that may strengthen farm-market linkages. An alternative recommended option is to continuously encourage farmers to do their own farm-records so that they will have more information for planning and managing risks in their next farm business activity.

Effect of the prebiotic fiber inulin on cholesterol metabolism in wildtype mice
Mistry, Rima H. ; Gu, Fangjie ; Schols, Henk A. ; Verkade, Henkjan J. ; Tietge, Uwe J.F. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Dietary non-digestible carbohydrates are perceived to improve health via gut microbiota-dependent generation of products such as short-chain fatty acids (SCFA). In addition, SCFA are also precursors for lipid and cholesterol synthesis potentially resulting in unwanted effects on lipid metabolism. Inulin is a widely used model prebiotic dietary fiber. Inconsistent reports on the effects of inulin on cholesterol homeostasis have emerged in humans and preclinical models. To clarify this issue, the present study aimed to provide an in-depth characterization of the effects of short-chain (sc)- and long-chain (lc)- inulin on cholesterol synthesis, absorption and elimination in mice. Feeding wildtype C57BL/6J mice diets supplemented with 10% (w/w) of either sc- or lc-inulin for two weeks resulted in approximately 2.5-fold higher fecal SCFA levels (P < 0.01) compared with controls, but had no significant effects on plasma and liver lipids. Subtle shifts in fecal and plasma bile acid species were detected with beta-muricholic acid increasing significantly in plasma of the inulin fed groups (1.7-fold, P < 0.05). However, neither sc-inulin nor lc-inulin affected intestinal cholesterol absorption, mass fecal cholesterol excretion or trans-intestinal cholesterol excretion (TICE). Combined, our data demonstrate that sc- and lc-inulin have no adverse effects on cholesterol metabolism in mice despite increased generation of SCFA.

Tipping points in adaptation to urban flooding under climate change and urban growth : The case of the Dhaka megacity
Ahmed, Farhana ; Moors, Eddy ; Khan, M.S.A. ; Warner, Jeroen ; Terwisscha van Scheltinga, Catharien - \ 2018
Land Use Policy 79 (2018). - ISSN 0264-8377 - p. 496 - 506.
Adaptation - Climate change, land use - Flood - Planning - Urban growth

Envisioning the future city as the outcome of planned development, several master and strategic plans for Dhaka were prepared. However, these plans, do not adequately address the well-known and combined effects of climate change and unplanned urbanization on urban flooding. Additionally, the spatial planning component is missing in adaptation planning, which broadly concentrates on the climate change. Long-term adaptation strategies should consider both the temporal and spatial extent of flooding. Uncertainties in climate change and urbanization will induce planning failure beyond the Adaptation Tipping Point for flooding exceeding the thresholds of the bio-physical system or the acceptable limits of societal preference. In this paper, a shift is proposed from the current planning practice of single-dimensional ‘Predict and Act’ towards a more resilience-based ‘Monitor and Adapt’ approach. It is prudent to visualize the effects of urbanization and climate change and translate them into strategies for improved adaptation based spatial planning. Here, Dhaka's exposure to floods under different climate change and urban (planned and unplanned) development scenarios is assessed based on acceptable thresholds obtained from plans (top-down defined) and stakeholders (bottom-up perspectives). The scale of effects of these two drivers on urban flooding is exhibited through the zone differentiated flooding extent. While apparently the effect of climate change on flooding is greater than that of unplanned urban developments, both play an important role in instigating tipping points and intensifying risks.

Meta-analysis of genome-wide association studies of aggressive and chronic periodontitis identifies two novel risk loci
Munz, Matthias ; Richter, Gesa M. ; Loos, Bruno G. ; Jepsen, Søren ; Divaris, Kimon ; Offenbacher, Steven ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Bruckmann, Corinna ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Ahmad, Ilyas ; Staufenbiel, Ingmar ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette C.P.G.M. De; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Laudes, Matthias ; Lieb, Wolfgang ; Franke, Andre ; Erdmann, Jeanette ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2018
European Journal of Human Genetics (2018). - ISSN 1018-4813
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. It is classified into the widespread moderate form chronic periodontitis (CP) and the rare early-onset and severe phenotype aggressive periodontitis (AgP). These different disease manifestations are thought to share risk alleles and predisposing environmental factors. To obtain novel insights into the shared genetic etiology and the underlying molecular mechanisms of both forms, we performed a two step-wise meta-analysis approach using genome-wide association studies of both phenotypes. Genotypes from imputed genome-wide association studies (GWAS) of AgP and CP comprising 5,095 cases and 9,908 controls of North-West European genetic background were included. Two loci were associated with periodontitis at a genome-wide significance level. They located within the pseudogene MTND1P5 on chromosome 8 (rs16870060-G, P = 3.69 × 10−9, OR = 1.36, 95% CI = [1.23–1.51]) and intronic of the long intergenic non-coding RNA LOC107984137 on chromosome 16, downstream of the gene SHISA9 (rs729876-T, P = 9.77 × 10−9, OR = 1.24, 95% CI = [1.15–1.34]). This study identified novel risk loci of periodontitis, adding to the genetic basis of AgP and CP.
Time for a European initiative for research to prevent cancer : A manifesto for Cancer Prevention Europe (CPE)
Forman, David ; Bauld, Linda ; Bonanni, Bernardo ; Brenner, Hermann ; Brown, Karen ; Dillner, Joakim ; Kampman, Ellen ; Manczuk, Marta ; Riboli, Elio ; Steindorf, Karen ; Storm, Hans ; Espina, Carolina ; Wild, Christopher P. - \ 2018
- p. 15 - 23.
Cancer prevention - Collaborative research - Europe - Health promotion - Knowledge hub - Multidisciplinary - Population-level - Translational research

A landmark resolution on cancer prevention and control was adopted by Member States at the World Health Assembly 2017, noting that “risk reduction has the potential to prevent around half of all cancers” and urging “to promote cancer research to improve the evidence base for cancer prevention and control”. Public health oriented strategies for cancer prevention and their optimal application in effective real-life programmes will be vital to circumvent the dramatic health and economic implications of a strategy and healthcare expenditure based primarily on cancer treatment. The inter-disciplinary nature of cancer prevention stretches from the sub-microscopic study of cancer pathways through to the supra-macroscopic analysis of the “causes of the causes” encompassing socio-economic and environmental factors. Research is required to provide new evidence-based preventive interventions and to understand the factors that hamper their implementation within health care systems and in the community. Successful implementation of cancer prevention requires long-term vision, a dedicated research agenda and funding, sustainable infrastructure and cooperation between countries and programmes. In order to develop world class prevention research in Europe that translates into effective cancer prevention guidelines and policies, we report on the creation of Cancer Prevention Europe. This international and multidisciplinary consortium of research institutes, organisations and networks of excellence with a common mission of reducing cancer morbidity and mortality in European populations through prevention, brings together different fields of expertise, from laboratory science through to policy research, as well as dissemination of the best evidence, the best quality indicators and the best practices used.

Grand challenges in soft matter physics
Gucht, Jasper van der - \ 2018
Active matter - Colloids - Non-equilibrium physics - Polymers - Self-assembly - Soft matter physics

As its name implies, soft matter science deals with materials that are easily deformed. These materials, which include polymers, gels, colloids, emulsions, foams, surfactant assemblies, liquid crystals, granular materials, and many biological materials, have in common that they are organized on mesoscopic length scales, with structural features that are much larger than an atom, but much smaller than the overall size of the material. The large size of the basic structural units and the relatively weak interactions that hold them together are responsible for the characteristic softness of these materials1, but they also lead to many other distinct features of soft materials [1], such as sensitivity toward thermal fluctuations and external stimuli and a slow response with long relaxation times, often resulting in non-trivial flow behavior and arrest in non-equilibrium states. These features make soft matter problems challenging. In hard condensed matter physics, it is often possible to accurately predict material properties based on the interactions between the individual atoms, which are typically organized on a regular crystalline lattice. For soft matter systems, with their intrinsically heterogeneous structure, complex interactions across different length scales, and slow dynamics, this is much more difficult. The subtle interplay between interactions and thermal fluctuations can lead to complex emergent behavior, such as spontaneous pattern formation, self-assembly, and a large response to small external stimuli. Because of the wide range of materials and systems that can be classified as soft matter, soft matter science is an inherently interdisciplinary field, in which physics, chemistry, materials science, biology, nanotechnology, and engineering come together. For a field that is so broad in scope, it is impossible to do justice to the entire range of outstanding problems or even to identify two or three key challenges. For this reason, I will only highlight a small (and highly personal) selection of current challenges in the field. The interdisciplinary nature of the field will be evident from these examples.

Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities
Harkes, Paula - \ 2018
The impact of soil pathogens on crops has been studied for decades as if this was a multitude of bilateral interactions. For a long time, it has been realised that crops and soil-borne pathogens are interacting in a densely inhabited environment, the rhizosphere. A more versatile approach was hampered because of technical limitations: it was just impracticable to take major and highly diverse organismal groups such as bacteria, fungi and protists into consideration. Here we monitored the (plant-parasitic) nematode community in the rhizosphere of barley under three distinct soil management regimes, for two developmental stages of the crop, in two different locations. Total DNA and RNA was isolated from rhizosphere samples - 104 rhizosphere samples, for each sample DNA and cDNA was analysed separately - using home-made extraction and purification protocols. Targeted (ribosomal DNA) Illumina MiSeq sequencing was used to characterise the nematode, protist, fungal and bacterial community. First of all, very significant location effects were observed for all four organismal groups. Superimposed on the location effects, clear effects of organic, integrated and conventional soil management could be pinpointed. To the best of our knowledge, this is the first time four major key organismal groups players of the soil food web are simultaneously mapped in order to obtain insight in the effects of soil management practices on plant-parasitic nematodes taking a major part of the rhizobiome into consideration.
Regionalisation in poultry developmen in Eastern Africa
Vernooij, Adriaan ; Masaki, Mackenzie N. ; Meijer-Willems, Daphne - \ 2018
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1121) - 47
This regional study of East Africa’s (EA) poultry sector was commissioned by the Food and Business Knowledge platform in 2017 with deference to the growing interest of Dutch companies in East Africa. The poultry sector in EA has been growing rapidly for the past 5 years driven by: rapid urbanization; the growth of the middle class in EA; rise in number of quick services restaurants in urban areas in EA; and growing need for animal protein. Of the four EA economies, Kenya’s poultry sector is the most mature. However, all the other three economies have in the past five years made significant strides towards developing and growing their own poultry sector.In order to justify the case for regional approach to poultry development in EA 3 key issues were addressed. First the availability and production of good quality feed at competitive prices. Governments in the region have made conscious policy changes to incentivize the import of raw materials and ingredients for feed into the region. In addition to this certain countries in EA such as Tanzania and Rwanda have made poultry specific strategies to catalyse growth of their poultry sectors. Whereas collective initiatives are in principal good for sectoral development at a regional level, history shows that there are the significant challenges to overcome. For instance, clarity on cross border trade in maize, oil seeds and oil seed cake is necessary for a sound regional approach to feed. The disparity in terms of available land for maize cultivation, the cost price and eventual market price for maize differs significantly per country in EA. Each county in EA has a competitive advantage that could complement the others. However, finding these complementarities and capitalising them for the greater good of the region will give rise to significant benefits for each EA member state. Secondly, the availability of DOCs across EA is a challenge. Kenya trades with Uganda and Uganda trades with Rwanda when it comes to DOCs. There is a shortage of DOCs in EA and there is a seasonality both in availability and price that makes it difficult for farmers to plan ahead and manage their costs.Lastly, access to markets, the East African Community (EAC) is both an economic and political block. Citizens of the member states are in principal allowed to work, do business and trade with one another freely. Though the EAC is the most advanced regional economic block in Africa it still faces certain challenges to implementing certain policies collectively. For instance in February of 2018 all EA member states agreed to remove VAT on all raw materials imported for feed manufacturing. Of the four member states, three have already tabled this policy in parliament and one has not. Free access to a market of approximately 140 million people will drive investments in the sector across the entire value chain. Such initiatives should be given priority and expedited in order to catalyse investments and growth in the EA poultry sector.Complimentary to the three issues above is knowledge and training at vocational and tertiary levels in EA. There is need for better more specific training and education in the poultry sector. A case in point is in EA veterinary doctors are in principal experts for all livestock and poultry is one amongst many of the courses they would take during their 4 to 6 years study. Upon completion most are not equipped to immediately enter into the poultry sector. Most farms and companies in the sector have been forced to develop on the job training programs that allow high performers to learn poultry specific knowledge. In addition to knowledge and training collective investment in regulation and enforcement of good biosecurity and animal health practices would go a long way to reduce and or manage disease outbreaks in the region. In the context of this study, it is observed that in EA a majority of poultry farmers are either small or medium scale farmers. Collective investments in feed, DOCs, animal health, knowledge transfer, capacity building, training and access to markets will greatly assist them become better farmers. In recognition of the increased significance of the poultry sector, various financing and financial institutions have become interested in poultry farmers and other poultry sector value chain actors.6 | Wageningen Livestock Research Report 1121These developments coupled with increasing demand for animal protein make the sector very attractive not only for local actors but also for the Dutch private sector.
Understanding meta-population trends of the Australian fur seal, with insights for adaptive monitoring
McIntosh, Rebecca R. ; Kirkman, Steve P. ; Thalmann, Sam ; Sutherland, Duncan R. ; Mitchell, Anthony ; Arnould, John P.Y. ; Salton, Marcus ; Slip, David J. ; Dann, Peter ; Kirkwood, Roger - \ 2018
PLoS One 13 (2018)9. - ISSN 1932-6203 - p. e0200253 - e0200253.
Effective ecosystem-based management requires estimates of abundance and population trends of species of interest. Trend analyses are often limited due to sparse or short-term abundance estimates for populations that can be logistically difficult to monitor over time. Therefore it is critical to assess regularly the quality of the metrics in long-term monitoring programs. For a monitoring program to provide meaningful data and remain relevant, it needs to incorporate technological improvements and the changing requirements of stakeholders, while maintaining the integrity of the data. In this paper we critically examine the monitoring program for the Australian fur seal (AFS) Arctocephalus pusillus doriferus as an example of an ad-hoc monitoring program that was co-ordinated across multiple stakeholders as a range-wide census of live pups in the Austral summers of 2002, 2007 and 2013. This 5-yearly census, combined with historic counts at individual sites, successfully tracked increasing population trends as signs of population recovery up to 2007. The 2013 census identified the first reduction in AFS pup numbers (14,248 live pups, -4.2% change per annum since 2007), however we have limited information to understand this change. We analyse the trends at breeding colonies and perform a power analysis to critically examine the reliability of those trends. We then assess the gaps in the monitoring program and discuss how we may transition this surveillance style program to an adaptive monitoring program than can evolve over time and achieve its goals. The census results are used for ecosystem-based modelling for fisheries management and emergency response planning. The ultimate goal for this program is to obtain the data we need with minimal cost, effort and impact on the fur seals. In conclusion we identify the importance of power analyses for interpreting trends, the value of regularly assessing long-term monitoring programs and proper design so that adaptive monitoring principles can be applied.
Data from: The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity
Bortoluzzi, C. ; Crooijmans, R.P.M.A. ; Bosse, M. ; Hiemstra, S.J. ; Groenen, M. ; Megens, H.J.W.C. - \ 2018
bantam - biodiversity - chicken - genetic diversity - molecular characterisation - traditional breed
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.
Dependency of Antarctic zooplankton species on ice algae-produced carbon suggests a sea ice-driven pelagic ecosystem during winter
Kohlbach, Doreen ; Graeve, Martin ; Lange, Benjamin A. ; David, Carmen ; Schaafsma, Fokje L. ; Franeker, Jan Andries van; Vortkamp, Martina ; Brandt, Angelika ; Flores, Hauke - \ 2018
Global Change Biology (2018). - ISSN 1354-1013
Antarctic food web - carbon sources - climate change - Compound-specific Stable Isotope Analysis - marker fatty acids - sea ice algae - under-ice community

How the abundant pelagic life of the Southern Ocean survives winter darkness, when the sea is covered by pack ice and phytoplankton production is nearly zero, is poorly understood. Ice-associated (“sympagic”) microalgae could serve as a high-quality carbon source during winter, but their significance in the food web is so far unquantified. To better understand the importance of ice algae-produced carbon for the overwintering of Antarctic organisms, we investigated fatty acid (FA) and stable isotope compositions of 10 zooplankton species, and their potential sympagic and pelagic carbon sources. FA-specific carbon stable isotope compositions were used in stable isotope mixing models to quantify the contribution of ice algae-produced carbon (αIce) to the body carbon of each species. Mean αIce estimates ranged from 4% to 67%, with large variations between species and depending on the FA used for the modelling. Integrating the αIce estimates from all models, the sympagic amphipod Eusirus laticarpus was the most dependent on ice algal carbon (αIce: 54%–67%), and the salp Salpa thompsoni showed the least dependency on ice algal carbon (αIce: 8%–40%). Differences in αIceestimates between FAs associated with short-term vs. long-term lipid pools suggested an increasing importance of ice algal carbon for many species as the winter season progressed. In the abundant winter-active copepod Calanus propinquus, mean αIce reached more than 50% in late winter. The trophic carbon flux from ice algae into this copepod was between 3 and 5 mg C m−2 day−1. This indicates that copepods and other ice-dependent zooplankton species transfer significant amounts of carbon from ice algae into the pelagic system, where it fuels the food web, the biological carbon pump and elemental cycling. Understanding the role of ice algae-produced carbon in these processes will be the key to predictions of the impact of future sea ice decline on Antarctic ecosystem functioning.

Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia
Fulgione, Andrea ; Koornneef, Maarten ; Roux, Fabrice ; Hermisson, Joachim ; Hancock, Angela M. - \ 2018
Molecular Biology and Evolution 35 (2018)3. - ISSN 0737-4038 - p. 564 - 574.
Admixture - Arabidopsis thaliana - Demography - Island - Population genetics - Relict

The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersal model (of size 10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).

The red bayberry genome and genetic basis of sex determination
Jia, Hui Min ; Jia, Hui Juan ; Cai, Qing Le ; Wang, Yan ; Zhao, Hai Bo ; Yang, Wei Fei ; Wang, Guo Yun ; Li, Ying Hui ; Zhan, Dong Liang ; Shen, Yu Tong ; Niu, Qing Feng ; Chang, Le ; Qiu, Jie ; Zhao, Lan ; Xie, Han Bing ; Fu, Wan Yi ; Jin, Jing ; Li, Xiong Wei ; Jiao, Yun ; Zhou, Chao Chao ; Tu, Ting ; Chai, Chun Yan ; Gao, Jin Long ; Fan, Long Jiang ; Weg, Eric van de; Wang, Jun Yi ; Gao, Zhong Shan - \ 2018
Plant Biotechnology Journal (2018). - ISSN 1467-7644
genome - Morella rubra - sex-determining region - sex-linked marker

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

Multidecadal, county-level analysis of the effects of land use, Bt cotton, and weather on cotton pests in China
Zhang, Wei ; Lu, Yanhui ; Werf, Wopke van der; Huang, Jikun ; Wu, Feng ; Zhou, Ke ; Deng, Xiangzheng ; Jiang, Yuying ; Wu, Kongming ; Rosegrant, Mark W. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)33. - ISSN 0027-8424 - p. E7700 - E7709.
Bt-cotton - Climate change - Insecticide use - Integrated pest management - Land use diversity

Long-term changes in land use, climate, and agricultural technologies may affect pest severity and management. The influences of these major drivers can only be identified by analyzing long-term data. This study examines panel data on land use, adoption of genetically modified Bacillus thuringiensis (Bt) insect-resistant cotton, weather, pest severity, and insecticide use on three major cotton pests for 51 counties in China during 1991–2015. Bt cotton had pervasive effects on the whole pest complex in cotton and its management. Adoption resulted in major reductions in insecticide use for bollworm control. The resulting restoration of aphid biological control decreased aphid severity. However, mirid bugs, which have few effective natural enemies in cotton, increased in severity with warming May and reduced insecticide spraying against bollworm. The effects of landscape on pest severity were pest specific. The severity of cotton aphid and mirid bugs decreased with higher land use diversity, but the severity of highly polyphagous cotton bollworm was unrelated to land use diversity. Shares of forest, water body, and unused land area were negatively associated with the severity of mirid bugs, whereas cotton bollworm responded positively to the shares of water body and unused land area. Farmers sprayed insecticides at mild infestation levels and responded aggressively to severe bollworm outbreaks. Findings support the usefulness of Bt-based plant resistance as a component of integrated pest management (IPM) but highlight the potential for unexpected outcomes resulting from agro-ecosystem feedback loops as well as the importance of climate.

Force-transmitting structures in the digital pads of the tree frog Hyla cinerea : a functional interpretation
Langowski, Julian K.A. ; Schipper, Henk ; Blij, Anne ; Berg, Frank T. van den; Gussekloo, Sander W.S. ; Leeuwen, Johan L. van - \ 2018
Journal of anatomy 233 (2018)4. - ISSN 0021-8782 - p. 478 - 495.
attachment organ - bioadhesion - collagen - connective tissue - fibre-matrix-composite - material stiffness - shear load - smooth muscle

The morphology of the digital pads of tree frogs is adapted towards attachment, allowing these animals to attach to various substrates and to explore their arboreal habitat. Previous descriptions and functional interpretations of the pad morphology mostly focussed on the surface of the ventral epidermis, and little is known about the internal pad morphology and its functional relevance in attachment. In this study, we combine histology and synchrotron micro-computer-tomography to obtain a comprehensive 3-D morphological characterisation of the digital pads (in particular of the internal structures involved in the transmission of attachment forces from the ventral pad surface towards the phalanges) of the tree frog Hyla cinerea. A collagenous septum runs from the distal tip of the distal phalanx to the ventral cutis and compartmentalises the subcutaneous pad volume into a distal lymph space and a proximal space, which contains mucus glands opening via long ducts to the ventral pad surface. A collagen layer connects the ventral basement membrane via interphalangeal ligaments with the middle phalanx. The collagen fibres forming this layer curve around the transverse pad-axis and form laterally separated ridges below the gland space. The topological optimisation of a shear-loaded pad model using finite element analysis (FEA) shows that the curved collagen fibres are oriented along the trajectories of the maximum principal stresses, and the optimisation also results in ridge-formation, suggesting that the collagen layer is adapted towards a high stiffness during shear loading. We also show that the collagen layer is strong, with an estimated tensile strength of 2.0–6.5 N. Together with longitudinally skewed tonofibrils in the superficial epidermis, these features support our hypothesis that the digital pads of tree frogs are primarily adapted towards the generation and transmission of friction rather than adhesion forces. Moreover, we generate (based on a simplified FEA model and predictions from analytical models) the hypothesis that dorsodistal pulling on the collagen septum facilitates proximal peeling of the pad and that the septum is an adaptation towards detachment rather than attachment. Lastly, by using immunohistochemistry, we (re-)discovered bundles of smooth muscle fibres in the digital pads of tree frogs. We hypothesise that these fibres allow the control of (i) contact stresses at the pad–substrate interface and peeling, (ii) mucus secretion, (iii) shock-absorbing properties of the pad, and (iv) the macroscopic contact geometry of the ventral pad surface. Further work is needed to conclude on the role of the muscular structures in tree frog attachment. Overall, our study contributes to the functional understanding of tree frog attachment, hence offering novel perspectives on the ecology, phylogeny and evolution of anurans, as well as the design of tree-frog-inspired adhesives for technological applications.

What is the role of the model in socio-hydrology? Discussion of “Prediction in a socio-hydrological world”*
Melsen, Lieke Anna ; Vos, Jeroen ; Boelens, Rutgerd - \ 2018
Hydrological Sciences Journal (2018). - ISSN 0262-6667
modelling - prediction - socio-hydrology - socio-natural relationships - transdisciplinarity

Srinivasan et al. provide an interesting overview of the challenges for long-term socio-hydrological predictions. Although agreeing with most of the statements made, we argue for the need to take socio-hydrological analysis a step further and add some fundamental considerations, especially concerning the crucial importance of many (conscious and unconscious) assumptions made upfront of the modelling exercise. Eventual assumptions of technological determinism need correction: Models are not “value-free”, but uncertain, subjective and a product of the society in which they were shaped. It is important to acknowledge this uncertainty and bias when making decisions based on socio-hydrological models, considering also that these models are “social and political actors” in and by themselves. Furthermore, socio-hydrological models require a transdisciplinary approach, since physical water availability is only one of the boundary conditions for society. Last but not least, interaction with stakeholders remains important to enable understanding of what the variable of interest is.

Making salt-reduced products more appealing to consumers : Impact of front-of-pack messages on liking and table salt use over time
Zandstra, Elizabeth H. ; Willems, Astrid A. ; Lion, René - \ 2018
Public Health Nutrition (2018). - ISSN 1368-9800
Labelling - Long-term liking - Salt perception - Salt reduction - Table salt use
Objective: The current study investigated the impact of different front-of-pack messages on liking, salt perception and table salt use of salt-reduced soups over repeated consumption. Design: In a between-subjects design, participants consumed a chicken noodle soup five times over 3 weeks. Participants were assigned to one of five experimental conditions and were categorized into three 'Interest in Salt Reduction' groups based on their self-reported interest in salt reduction. They consumed a regular-salt soup or a 30 % salt-reduced soup, either with or without a front-of-pack message (nutritional, sensory or social based). Liking, salt perception and table salt use were measured at each consumption. Setting: Central location test. Subjects: British consumers (n 493) aged 24-65 years. Results: The soups remained stable in liking over repeated consumption, with no significant differences between the experimental conditions. However, liking did differ among the different Interest in Salt Reduction groups: the 'not aware, no action' group liked salt-reduced soups with a nutritional message the most, whereas the 'aware and action' group liked salt-reduced soups with a social message the most. There was no change in the amount of table salt added as people got more familiar with the salt-reduced soups, suggesting a strong role for habit in table salt use. Conclusions: It mattered whether consumers were thinking about reducing their salt intake or not: a communication message tailored to a country's interest in reducing salt is recommended to motivate consumers to lower their salt intake.
Top-down NOx emissions of european cities based on the downwind plume of modelled and space-borne tropospheric NO2 columns
Verstraeten, Willem W. ; Boersma, Klaas Folkert ; Douros, John ; Williams, Jason E. ; Eskes, Henk ; Liu, Fei ; Beirle, Steffen ; Delcloo, Andy - \ 2018
Sensors 18 (2018)9. - ISSN 1424-8220
LOTOS-EUROS CTM - OMI data - Surface NO emissions - Tropospheric NO column

Top-down estimates of surface NOX emissions were derived for 23 European cities based on the downwind plume decay of tropospheric nitrogen dioxide (NO2) columns from the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) chemistry transport model (CTM) and from Ozone Monitoring Instrument (OMI) satellite retrievals, averaged for the summertime period (April–September) during 2013. Here we show that the top-down NOX emissions derived from LOTOS-EUROS for European urban areas agree well with the bottom-up NOX emissions from the MACC-III inventory data (R2 = 0.88) driving the CTM demonstrating the potential of this method. OMI top-down NOX emissions over the 23 European cities are generally lower compared with the MACC-III emissions and their correlation is slightly lower (R2 = 0.79). The uncertainty on the derived NO2 lifetimes and NOX emissions are on average ~55% for OMI and ~63% for LOTOS-EUROS data. The downwind NO2 plume method applied on both LOTOS-EUROS and OMI tropospheric NO2 columns allows to estimate NOX emissions from urban areas, demonstrating that this is a useful method for real-time updates of urban NOX emissions with reasonable accuracy.

Environmental and taxonomic controls of carbon and oxygen stable isotope composition in Sphagnum across broad climatic and geographic ranges
Granath, Gustaf ; Rydin, Håkan ; Baltzer, Jennifer L. ; Bengtsson, Fia ; Boncek, Nicholas ; Bragazza, Luca ; Bu, Zhao Jun ; Caporn, Simon J.M. ; Dorrepaal, Ellen ; Galanina, Olga ; GaÅka, Mariusz ; Ganeva, Anna ; Gillikin, David P. ; Goia, Irina ; Goncharova, Nadezhda ; Hájek, Michal ; Haraguchi, Akira ; Harris, Lorna I. ; Humphreys, Elyn ; Jiroušek, Martin ; KajukaÅo, Katarzyna ; Karofeld, Edgar ; Koronatova, Natalia G. ; Kosykh, Natalia P. ; Lamentowicz, Mariusz ; Lapshina, Elena ; Limpens, Juul ; Linkosalmi, Maiju ; Ma, Jin Ze ; Mauritz, Marguerite ; Munir, Tariq M. ; Natali, Susan M. ; Natcheva, Rayna ; Noskova, Maria ; Payne, Richard J. ; Pilkington, Kyle ; Robinson, Sean ; Robroek, Bjorn J.M. ; Rochefort, Line ; Singer, David ; Stenøien, Hans K. ; Tuittila, Eeva Stiina ; Vellak, Kai ; Verheyden, Anouk ; Michael Waddington, James ; Rice, Steven K. - \ 2018
Biogeosciences 15 (2018)16. - ISSN 1726-4170 - p. 5189 - 5202.

Rain-fed peatlands are dominated by peat mosses (Sphagnum sp.), which for their growth depend on nutrients, water and CO2 uptake from the atmosphere. As the isotopic composition of carbon (12,13C) and oxygen (16,18O) of these Sphagnum mosses are affected by environmental conditions, Sphagnum tissue accumulated in peat constitutes a potential long-term archive that can be used for climate reconstruction. However, there is inadequate understanding of how isotope values are influenced by environmental conditions, which restricts their current use as environmental and palaeoenvironmental indicators. Here we tested (i) to what extent C and O isotopic variation in living tissue of Sphagnum is species-specific and associated with local hydrological gradients, climatic gradients (evapotranspiration, temperature, precipitation) and elevation; (ii) whether the C isotopic signature can be a proxy for net primary productivity (NPP) of Sphagnum; and (iii) to what extent Sphagnum tissue δ18O tracks the δ18O isotope signature of precipitation. In total, we analysed 337 samples from 93 sites across North America and Eurasia using two important peat-forming Sphagnum species (S. magellanicum, S. fuscum) common to the Holarctic realm. There were differences in δ13C values between species. For S. magellanicum δ13C decreased with increasing height above the water table (HWT, R2 =17%) and was positively correlated to productivity (R2 = 7%). Together these two variables explained 46% of the between-site variation in δ13C values. For S. fuscum, productivity was the only significant predictor of δ13C but had low explanatory power (total R2 = 6%). For δ18O values, approximately 90% of the variation was found between sites. Globally modelled annual δ18O values in precipitation explained 69% of the between-site variation in tissue δ18O. S. magellanicum showed lower δ18O enrichment than S. fuscum (-0.83 ‰ lower). Elevation and climatic variables were weak predictors of tissue δ18O values after controlling for δ18O values of the precipitation. To summarize, our study provides evidence for (a) good predictability of tissue δ18O values from modelled annual δ18O values in precipitation, and (b) the possibility of relating tissue δ13C values to HWT and NPP, but this appears to be species-dependent. These results suggest that isotope composition can be used on a large scale for climatic reconstructions but that such models should be species-specific.

Plant species richness and functional groups have different effects on soil water content in a decade-long grassland experiment
Fischer, Christine ; Leimer, Sophia ; Roscher, Christiane ; Ravenek, Janneke ; Kroon, Hans de; Kreutziger, Yvonne ; Baade, Jussi ; Beßler, Holger ; Eisenhauer, Nico ; Weigelt, Alexandra ; Mommer, Liesje ; Lange, Markus ; Gleixner, Gerd ; Wilcke, Wolfgang ; Schröder, Boris ; Hildebrandt, Anke - \ 2018
Journal of Ecology (2018). - ISSN 0022-0477
biodiversity - functional groups - Jena Experiment - plant–soil–water relation - soil water content - spatial–temporal variability - species richness

The temporal and spatial dynamics of soil water are closely interlinked with terrestrial ecosystems functioning. The interaction between plant community properties such as species composition and richness and soil water mirrors fundamental ecological processes determining above-ground–below-ground feedbacks. Plant–water relations and water stress have attracted considerable attention in biodiversity experiments. Yet, although soil scientific research suggests an influence of ecosystem productivity on soil hydraulic properties, temporal changes of the soil water content and soil hydraulic properties remain largely understudied in biodiversity experiments. Thus, insights on how plant diversity—productivity relationships affect soil water are lacking. Here, we determine which factors related to plant community composition (species and functional group richness, presence of plant functional groups) and soil (organic carbon concentration) affect soil water in a long-term grassland biodiversity experiment (The Jena Experiment). Both plant species richness and the presence of particular functional groups affected soil water content, while functional group richness played no role. The effect of species richness changed from positive to negative and expanded to deeper soil with time. Shortly after establishment, increased topsoil water content was related to higher leaf area index in species-rich plots, which enhanced shading. In later years, higher species richness increased topsoil organic carbon, likely improving soil aggregation. Improved aggregation, in turn, dried topsoils in species-rich plots due to faster drainage of rainwater. Functional groups affected soil water distribution, likely due to plant traits affecting root water uptake depths, shading, or water-use efficiency. For instance, topsoils in plots containing grasses were generally drier, while plots with legumes were moister. Synthesis. Our decade-long experiment reveals that the maturation of grasslands changes the effects of plant richness from influencing soil water content through shading effects to altering soil physical characteristics in addition to modification of water uptake depth. Functional groups affected the soil water distribution by characteristic shifts of root water uptake depth, but did not enhance exploitation of the overall soil water storage. Our results reconcile previous seemingly contradictory results on the relation between grassland species diversity and soil moisture and highlight the role of vegetation composition for soil processes.

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