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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    Gut dysbacteriosis and intestinal disease: mechanism and treatment
    Meng, X. ; Zhang, G. ; Cao, H. ; Yu, D. ; Fang, X. ; Vos, W.M. de; Wu, H. - \ 2020
    Journal of Applied Microbiology (2020). - ISSN 1364-5072
    gut microbiome - immune response - intestinal diseases - prebiotics - probiotics

    The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota–derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.

    Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs
    Cao, Lu ; Liu, Huiming ; Mulder, Han A. ; Henryon, Mark ; Thomasen, Jørn Rind ; Kargo, Morten ; Sørensen, Anders Christian - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    across-environment selection of sires - genetic gain - joint genetic evaluation - long-term cooperation - rate of inbreeding - stochastic simulation

    Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (rg) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point rg that is the lowest value of rg for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point rg than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

    Can pedotransfer functions based on environmental variables improve soil total nutrient mapping at a regional scale?
    Song, Xiao Dong ; Rossiter, David G. ; Liu, Feng ; Wu, Hua Yong ; Zhao, Xiao Rui ; Cao, Qi ; Zhang, Gan Lin - \ 2020
    Soil & Tillage Research 202 (2020). - ISSN 0167-1987
    Digital soil mapping - Random forest - Regression analysis - Total nitrogen - Total phosphorus - Total potassium

    Numerous pedotransfer functions (PTFs) have been developed to predict the soil properties of interest from other soil properties and, less commonly, from environmental variables. However, only a few PTFs have been developed to predict soil nutrients using environmental variables and to extrapolate them to characterize spatial soil variations at a regional scale. In this study, we attempted to develop PTFs for the total nitrogen (TN), total phosphorus (TP) and total potassium (TK) concentrations in three typical pedo-climatic areas of China (Fujian Province, Jiangsu Province and Qilian Mountains) with diverse climate, terrain and soil types. A series of linear PTFs were developed to quantify the effect of terrain and climate on the predictive relations between the soil nutrients and other measured soil properties and environmental variables. In addition, digital soil mapping (DSM) based on the random forest (RF) technique was performed to test the hypothesis that the best-fit PTFs could be extrapolated, based on soil maps and environmental variables, to describe regional soil variations in the soil nutrients. The root mean square errors (RMSEs) of the best-fit PTFs for TN, TP and TK ranged from 0.21 to 0.79 g kg−1, 0.20 to 0.58 g kg−1, and 3.68 to 5.00 g kg−1, respectively. Different RMSEs were produced by DSM, namely 0.37-1.89 g kg−1, 0.19−0.56 g kg−1 and 3.79-4.83 g kg−1 for TN, TP and TK, respectively. PTFs provided a sound basis for database compilation if the soil properties were highly correlated. However, the extrapolation of best-fit PTFs to regional scales yielded greater errors than those produced by DSM. The comparison results reveal the limitations of PTFs and suggest that their performance could be improved by using environmental covariates or by fitting data in areas with relatively homogeneous soil landscapes. The DSM techniques may provide satisfactory alternatives to predict soil data at both regional and plot scales.

    Acidification of manure reduces gaseous emissions and nutrient losses from subsequent composting process
    Cao, Yubo ; Wang, Xuan ; Liu, Ling ; Velthof, Gerard L. ; Misselbrook, Tom ; Bai, Zhaohai ; Ma, Lin - \ 2020
    Journal of Environmental Management 264 (2020). - ISSN 0301-4797
    Composting - GHG emissions - Manure acidification - N balance - NH emission - P balance

    Manure acidification is recommended to minimize ammonia (NH3) emission at storage. However, the potential for acidification to mitigate NH3 emission from storage and the impact of manure acidification (pH range 5–8) on composting have been poorly studied. The effects of manure acidification at storage on the subsequent composting process, nutrient balance, gaseous emissions and product quality were assessed through an analysis of literature data and an experiment under controlled conditions. Results of the data mining showed that mineral acids, acidic salts and organic acids significantly reduced NH3 emission, however, a weaker effect was observed for organic acids. A subsequent composting experiment showed that using manure acidified to pH5 or pH6 as feedstock delayed organic matter degradation for 7–10 days, although pH6 had no negative effect on compost maturity. Acidification significantly decreased NH3 emission from both storage and composting, however, excessive acidification (pH5) enhanced N2O emissions (18.6%) during composting. When manure was acidified to pH6, N2O (17.6%) and CH4 (20%) emissions, and total GHG emissions expressed as global warming potential (GWP) (9.6%) were reduced during composting. Acidification of manure before composting conserved more N as NH4 + and NOx in compost product. Compared to the control, the labile, plant-available phosphorus (P) content in the compost product, predominately as water-soluble inorganic P, increased with manure acidification to pH5 and pH6. Acidification of manure to pH6 before composting decreases nutrient losses and gaseous emissions without decreasing the quality of the compost product. The techno-economic advantages of acidification should be further ascertained.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    Plant virus-derived nano-cages as delivery vehicle for DNA/RNA vaccination against spring viraemia of carp virus
    Goldman, Mark ; Cao, Shuqin - \ 2020
    In: WIAS Annual Conference 2020 WIAS - p. 31 - 31.
    Common carp (Cyprinus carpio) is one of the most cultured fish species worldwide. The increase in production, together with global intensification of aquaculture have led to infectious disease outbreaks. Disease prevention is therefore essential to prevent substantial economic losses and vaccination is currently the most efficient method for pathogen control. Common carp is susceptible to the highly contagious spring viraemia of carp virus(SVCV) and mortality can reach up to 70-90% in juvenile carp. Our laboratory successfully developed a DNA vaccine based on the SVCV glycoprotein. A single dose of 0.1μg DNA/gof fish led to up to 100% protection when injected intramuscularly. Unfortunately, the same vaccine did not confer protection when administered orally. In this project we investigated whether plant virus-derived virus-like particles (VLPs) can be used as a vehicle to deliver the DNA/RNA vaccine by immersion. Capsid proteins (CPs) of the plant virus cowpea chlorotic mottle virus (CCMV) were used to assemble VLPs containing our DNA/RNA vaccine.CCMV-VLPs are naturally not pathogenic to fish and are safe for the environment. CCMVCPs have the unique ability to reversibly disassemble and assemble by changing the pH,allowing us to replace the viral RNA for our DNA/RNA vaccine (cargo). We were able to successfully assemble VLPs with plasmid DNA and the VLPs were able to protect the plasmid DNA against DNase. Furthermore, VLPs were able to deliver the plasmid DNA to fishcells in vitro. Further studies will be performed on zebrafish to assess the uptake in vivo. The preliminary assessment of the suitability of CCMV-based VLPs as nucleic acids vaccine vehicle will be presented and discussed
    Impact of trends in river discharge and ocean tides on water level dynamics in the Pearl River Delta
    Cao, Yu ; Zhang, Wei ; Zhu, Yuliang ; Ji, Xiaomei ; Xu, Yanwen ; Wu, Yao ; Hoitink, A.J.F. - \ 2020
    Coastal Engineering 157 (2020). - ISSN 0378-3839
    Nonstationary harmonic analysis - River discharge - Tidal amplitudes - Tidal forcing - Water levels

    The spectrum of tidal and subtidal water level variations in river deltas responds to river discharge variation, ocean tides, and human activities of many kinds. It remains a contemporary challenge to identify the main sources of changes in tidal dynamics in deltas, because of nonlinear interactions between tides and the river discharge in a changing setting. Understanding the main forcing factors controlling the evolution of mean water levels and the associated amplitudes and phases of tidal constituents can help to understand the causes of floods and the occurrence of low flows hindering navigation. Here, a nonstationary harmonic analysis tool (NS_TIDE) is applied to hydrological data from 14 stations in the Pearl River Delta (PRD) spanning the period 1961–2012. The water levels and main tidal constituent properties are decomposed into contributions of external forcing by river discharges and ocean tides, providing insight into the nonstationary tidal-fluvial processes. Significant temporal trends in mean water levels and tidal properties are observed in the PRD. Results indicate that there is spatial variability in the response of mean water levels and tidal properties to river discharge variation in the delta. The abrupt changes in bathymetry in the delta due to intensive sand excavation are likely responsible for the observed spatial variations in tidal response, which reduce the flood-dominant tidal asymmetry in this area.

    PathBank: a comprehensive pathway database for model organisms
    Wishart, David S. ; Li, Carin ; Marcu, Ana ; Badran, Hasan ; Pon, Allison ; Budinski, Zachary ; Patron, Jonas ; Lipton, Debra ; Cao, Xuan ; Oler, Eponine ; Li, Krissa ; Paccoud, Maïlys ; Hong, Chelsea ; Guo, An C. ; Chan, Christopher ; Wei, William ; Ramirez-Gaona, Miguel - \ 2020
    Nucleic acids research 48 (2020)D1. - ISSN 0305-1048 - p. D470 - D478.

    PathBank (www.pathbank.org) is a new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli and Pseudomonas aeruginosa). PathBank aims to provide a pathway for every protein and a map for every metabolite. This resource is designed specifically to support pathway elucidation and pathway discovery in transcriptomics, proteomics, metabolomics and systems biology. It provides detailed, fully searchable, hyperlinked diagrams of metabolic, metabolite signaling, protein signaling, disease, drug and physiological pathways. All PathBank pathways include information on the relevant organs, organelles, subcellular compartments, cofactors, molecular locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to the rich data contained in public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All PathBank pathways are accompanied with references and detailed descriptions which provide an overview of the pathway, condition or processes depicted in each diagram. Every PathBank pathway is downloadable in several machine-readable and image formats including BioPAX, SBML, PWML, SBGN, RXN, PNG and SVG. PathBank also supports community annotations and submissions through the web-based PathWhiz pathway illustrator. The vast majority of PathBank's pathways (>95%) are not found in any other public pathway database.

    Genomic selection breeding program benefits more than traditional one in presence of G×E
    Cao, Lu ; Liu, H. ; Mulder, H.A. ; Henryon, Mark ; Thomasen, Jørn Rind ; Kargo, M. ; Sorensen, A.C. - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP Book of Abstracts ) - ISBN 9789086863396 - p. 528 - 528.
    Loss of functional connectivity in migration networks induces population decline in migratory birds
    Xu, Yanjie ; Si, Yali ; Wang, Yingying ; Zhang, Yong ; Prins, Herbert H.T. ; Cao, Lei ; Boer, Willem F. de - \ 2019
    Ecological Applications 29 (2019)7. - ISSN 1051-0761 - p. e01960 - e01960.
    bird migration - habitat loss - life history - network robustness - population dynamics - species traits - wetland

    Migratory birds rely on a habitat network along their migration routes by temporarily occupying stopover sites between breeding and non-breeding grounds. Removal or degradation of stopover sites in a network might impede movement and thereby reduce migration success and survival. The extent to which the breakdown of migration networks, due to changes in land use, impacts the population sizes of migratory birds is poorly understood. We measured the functional connectivity of migration networks of waterfowl species that migrate over the East Asian-Australasian Flyway from 1992 to 2015. We analysed the relationship between changes in non-breeding population sizes and changes in functional connectivity, while taking into account other commonly considered species traits, using a phylogenetic linear mixed model. We found that population sizes significantly declined with a reduction in the functional connectivity of migration networks; no other variables were important. We conclude that the current decrease in functional connectivity, due to habitat loss and degradation in migration networks, can negatively and crucially impact population sizes of migratory birds. Our findings provide new insights into the underlying mechanisms that affect population trends of migratory birds under environmental changes. Establishment of international agreements leading to the creation of systematic conservation networks associated with migratory species' distributions and stopover sites may safeguard migratory bird populations.

    Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
    Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling - \ 2019
    GigaScience 8 (2019)9. - ISSN 2047-217X
    Castanea mollissima - annotation - evolution - genome assembly

    BACKGROUND: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

    Water for maize for pigs for pork: An analysis of inter-provincial trade in China
    Zhuo, La ; Liu, Yilin ; Yang, Hong ; Hoekstra, Arjen Y. ; Liu, Wenfeng ; Cao, Xinchun ; Wang, Mengru ; Wu, Pute - \ 2019
    Water Research 166 (2019). - ISSN 0043-1354
    Maize - Pork - Supply chain - Virtual water trade - Water footprint

    Trade in commodities implies trade in virtual water (VW), which refers to the water that was used to produce the traded goods. Various studies have quantified international or inter-provincial virtual water (VW) flows related to the trade in crops and animal products. Until date, however, no effort has been undertaken to understand how the water embodied in traded feed crops (trade stage TS1) will be transferred further because of trade in animal products (trade stage TS2). This is the first study showing this mechanism, in a case study in China for maize (the major pig feed) and pork (the dominant meat), considering the period 2000–2013. We estimate the annual green and blue water footprints in maize production and then quantify the inter-provincial VW flows related to trade in maize (TS1) and trade in maize embodied in pork (TS2). Results show that in TS1, maize-related VW flowed from the water-scarce North to the water-rich South, with an increase of 40% over the study period (from 43 to 61 billion m3 y−1). In TS2, about 10% of the water embodied in maize exports from North to South China returns in the form of pork, with an increase in the absolute amount of 25% (from 4.8 to 6.1 billion m3 y−1). Considering blue VW flows specifically, we find that North-to-South blue VW flows decreased by 5% in TS1, while South-to-North blue VW flows increased by 23% in TS2.

    Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
    Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
    forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

    Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

    Integration of LCC and LCA results to higher system levels : The German meat and EU tomato cases
    Liu, Gang ; Xue, Li ; Cao, Zhi ; Prass, Neele ; Gollnow, Sebastian ; Davis, Jennifer ; Scherhaufer, Silvia ; Ostergren, Karin ; Menna, Fabio De ; Garcia Herrero, Laura ; Vittuari, Matteo ; Broeze, J. - \ 2019
    Wageningen : REFRESH - ISBN 9789463950015 - 112
    Wintering Swan Geese maximize energy intake through substrate foraging depth when feeding on buried Vallisneria natans tubers 06 Biological Sciences 0602 Ecology
    Chen, Yan ; Zhang, Yong ; Cao, Lei ; Boer, Willem F. De; Fox, Anthony D. - \ 2019
    Avian Research 10 (2019)1. - ISSN 2053-7166
    Energetic trade-off - Optimal foraging - Shengjin Lake - Substrate - Tuber burial depth - Yangtze River

    Background: Foraging theory predicts that animals select patches that offer the highest net rate of energy gain. Hence, prey distribution patterns and spatiotemporal heterogeneity play important roles in determining animal feeding patch selection. For waterfowl foraging on buried aquatic plant tubers, the distribution and biomass of these plant organs vary with depth in the substrate. Since excavation costs also increase with depth, the energy intake of the animals foraging on these plants is highly sediment depth dependent. Methods: Here, using observations of Swan Geese (Anser cygnoides) foraging on Vallisneria natans tubers, we test our hypothesis that geese feeding on tubers buried at intermediate sediment depth maximize their daily energy intake because of the interaction between tuber size and abundance with depth. To do this, we measured the distribution patterns of buried Vallisneria tubers under both undisturbed conditions and post-exploitation by geese (i.e. giving-up conditions). We investigated the relationship between tuber size and burial depth, and total tuber biomass within each sediment layer in undisturbed and exploited plots. Finally, we compared modelled Swan Goose daily energy intake feeding on Vallisneria tubers buried at different sediment layers (1-10, 11-20 and 21-30 cm below the surface). Results: Dry weight of Vallisneria tubers linearly increased with burial depth, while average total dry weight density of tubers showed a unimodal relationship, peaking at intermediate levels. Not surprisingly, Swan Geese foraged most intensively on tubers buried at intermediate sediment depths, where they maximize their daily energy intake. Our results support our hypothesis that Swan Geese feeding on tubers at intermediate depths maximize their daily energy intake. Conclusions: Our study is the first to quantify foraging strategies of Swan Geese during the wintering period, emphasizing the importance of plant traits on foraging selection of belowground foragers.

    Dystrophin is required for normal synaptic gain in the Drosophila olfactory circuit
    Jantrapirom, Salinee ; Cao, De Shou ; Wang, Jing W. ; Hing, Huey ; Tabone, Christopher J. ; Lantz, Kathryn ; Belle, J.S. de; Qiu, Yu Tong ; Smid, Hans M. ; Yamaguchi, Masamitsu ; Fradkin, Lee G. ; Noordermeer, Jasprina N. ; Potikanond, Saranyapin - \ 2019
    Brain Research 1712 (2019). - ISSN 0006-8993 - p. 158 - 166.
    Antennal lobe - Behavior - Drosophila melanogaster - Dystrophin - Olfaction - Olfactory receptor neurons - Projection neurons

    The Drosophila olfactory system provides an excellent model to elucidate the neural circuits that control behaviors elicited by environmental stimuli. Despite significant progress in defining olfactory circuit components and their connectivity, little is known about the mechanisms that transfer the information from the primary antennal olfactory receptor neurons to the higher order brain centers. Here, we show that the Dystrophin Dp186 isoform is required in the olfactory system circuit for olfactory functions. Using two-photon calcium imaging, we found the reduction of calcium influx in olfactory receptor neurons (ORNs) and also the defect of GABA A mediated inhibitory input in the projection neurons (PNs) in Dp186 mutation. Moreover, the Dp186 mutant flies which display a decreased odor avoidance behavior were rescued by Dp186 restoration in the Drosophila olfactory neurons in either the presynaptic ORNs or the postsynaptic PNs. Therefore, these results revealed a role for Dystrophin, Dp 186 isoform in gain control of the olfactory synapse via the modulation of excitatory and inhibitory synaptic inputs to olfactory projection neurons.

    CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in Arabidopsis thaliana
    Zhang, Luosha ; Shi, Xiong ; Zhang, Yutao ; Wang, Jiajing ; Yang, Jingwei ; Ishida, Takashi ; Jiang, Wenqian ; Han, Xiangyu ; Kang, Jingke ; Wang, Xuening ; Pan, Lixia ; Lv, Shuo ; Cao, Bing ; Zhang, Yonghong ; Wu, Jinbin ; Han, Huibin ; Hu, Zhubing ; Cui, Langjun ; Sawa, Shinichiro ; He, Junmin ; Wang, Guodong - \ 2019
    Plant, Cell & Environment 42 (2019)3. - ISSN 0140-7791 - p. 1033 - 1044.
    ABA - CLE peptide - hydrogen peroxide - nitric oxide - stomatal closure

    CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.

    Improved ordering of perishables : The value of stock-age information
    Haijema, René ; Minner, Stefan - \ 2019
    International Journal of Production Economics 209 (2019). - ISSN 0925-5273 - p. 316 - 324.
    Food waste - Heuristics - Perishable inventory management - Simulation-based optimization - Stock-age dependent ordering

    Many supermarkets and retailers use computer assisted ordering (CAO) or automated order systems (ASO) to determine replenishment quantities. Traditionally, these systems are designed for non-perishables, and order quantities are set by (modified) base stock policies, determined according to the total number of units in stock, regardless of the ages of the products in stock. Today's technology allows the user to keep track of the age of inventories. In the last decade, a few so-called stock-age dependent order policies have been proposed. An optimal stock-age dependent policy may be computed by stochastic dynamic programming (SDP), but an SDP policy is hardly ever adopted in practice for two reasons: (1) the policy can only be computed if the underlying state space is not too large, and (2) the resulting policy can have a complicated structure. In practice, logistics managers prefer well structured policies they do understand, such as base stock policies (BSP). In this paper, we give an overview of existing stock-age dependent order policies and provide new stock-age dependent order policies. We present a simulation-based search procedure and suggest search ranges for setting optimal parameter values. For a broad set of 11,177 instances, we test the algorithm, compare these policies by simulation, and discuss the value of stock-age information. A new policy, named BSP-low-EW, performs close to optimal (SDP) and turns out to outperform all other policies in virtually all cases.

    Effects of ecological and anthropogenic factors on waterbird abundance at a Ramsar Site in the Yangtze River Floodplain
    Zhang, Yong ; Fox, Anthony D. ; Cao, Lei ; Jia, Qiang ; Lu, Changhu ; Prins, Herbert H.T. ; Boer, Willem F. de - \ 2019
    Ambio 48 (2019)3. - ISSN 0044-7447 - p. 293 - 303.
    Conservation - Feeding guilds - Waterbirds - Wetland management - Yangtze Wetlands

    Continuing declines in abundance of many waterbird species on wetland ecosystems require explanations to support effective management interventions. We used 6 year survey data from Shengjin Lake National Nature Reserve in the Yangtze River Floodplain, China, to study the effects of ecological and anthropogenic variables as determinants of waterbird species abundance. Our results showed that effects were guild-dependent, although distance to nearest human settlements had the largest adverse effects on bird abundance across all guilds. These results suggested that although the abundance of waterbird species could be affected by habitat conditions and buffalo grazing activities, Yangtze River Wetlands would most likely benefit most from reduced pressure from the proximity to the surrounding human population. We suggest that screening and/or restricting public access at some key sites may be the most cost-efficient way to restrict or reduce human activity in these wetlands, to improve the conservation status and wintering conditions for these waterbirds.

    Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, D. ; Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Gungor, Berivan ; Hartog, M.V. ; Hontelez, Jan ; Verver, J.W.G. ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
    Wageningen University & Research
    comparative genomics - copy number variation - evolution - nitrogen fixation - symbiosis - Parasponia andersonii - Parasponia rigada - Parasponia rugosa - Trema levigata - Trema orientalis - Trema tomentosa
    Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants
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