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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    Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis
    Freire-Rios, Alejandra ; Tanaka, Keita ; Crespo, Isidro ; Wijk, Elmar Van der; Sizentsova, Yana ; Levitsky, Victor ; Lindhoud, Simon ; Fontana, Mattia ; Hohlbein, Johannes ; Boer, D.R. ; Mironova, Victoria ; Weijers, Dolf - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)39. - ISSN 0027-8424 - p. 24557 - 24566.
    ARF transcription factors - Auxin - Plant biology - Protein-DNA interaction - Transcriptional regulation

    The hormone auxin controls many aspects of the plant life cycle by regulating the expression of thousands of genes. The transcriptional output of the nuclear auxin signaling pathway is determined by the activity of AUXIN RESPONSE transcription FACTORs (ARFs), through their binding to cis-regulatory elements in auxinresponsive genes. Crystal structures, in vitro, and heterologous studies have fueled a model in which ARF dimers bind with high affinity to distinctly spaced repeats of canonical AuxRE motifs. However, the relevance of this "caliper" model, and the mechanisms underlying the binding affinities in vivo, have remained elusive. Here we biochemically and functionally interrogate modes of ARF-DNA interaction. We show that a single additional hydrogen bond in Arabidopsis ARF1 confers high-affinity binding to individual DNA sites. We demonstrate the importance of AuxRE cooperativity within repeats in the Arabidopsis TMO5 and IAA11 promoters in vivo. Meta-analysis of transcriptomes further reveals strong genome-wide association of auxin response with both inverted (IR) and direct (DR) AuxRE repeats, which we experimentally validated. The association of these elements with auxininduced up-regulation (DR and IR) or down-regulation (IR) was correlated with differential binding affinities of A-class and B-class ARFs, respectively, suggesting a mechanistic basis for the distinct activity of these repeats. Our results support the relevance of highaffinity binding of ARF transcription factors to uniquely spaced DNA elements in vivo, and suggest that differential binding affinities of ARF subfamilies underlie diversity in cis-element function.

    UDP-glucosyltransferase UGT84B1 regulates the levels of indole-3-acetic acid and phenylacetic acid in Arabidopsis
    Aoi, Yuki ; Hira, Hayao ; Hayakawa, Yuya ; Liu, Hongquan ; Fukui, Kosuke ; Dai, Xinhua ; Tanaka, Keita ; Hayashi, Ken Ichiro ; Zhao, Yunde ; Kasahara, Hiroyuki - \ 2020
    Biochemical and Biophysical Research Communications 532 (2020)2. - ISSN 0006-291X - p. 244 - 250.
    Auxin - Indole-3-acetic acid - Metabolism - Phenylacetic acid - UDP-Glucosyltransferase

    Auxin is a key plant growth regulator for diverse developmental processes in plants. Indole-3-acetic acid (IAA) is a primary plant auxin that regulates the formation of various organs. Plants also produce phenylacetic acid (PAA), another natural auxin, which occurs more abundantly than IAA in various plant species. Although it has been demonstrated that the two auxins have distinct transport characteristics, the metabolic pathways and physiological roles of PAA in plants remain unsolved. In this study, we investigated the role of Arabidopsis UDP-glucosyltransferase UGT84B1 in IAA and PAA metabolism. We demonstrated that UGT84B1, which converts IAA to IAA-glucoside (IAA-Glc), can also catalyze the conversion of PAA to PAA-glucoside (PAA-Glc), with a higher catalytic activity in vitro. Furthermore, we showed a significant increase in both the IAA and PAA levels in the ugt84b1 null mutants. However, no obvious developmental phenotypes were observed in the ugt84b1 mutants under laboratory growth conditions. Moreover, the overexpression of UGT84B1 resulted in auxin-deficient root phenotypes and changes in the IAA and PAA levels. Our results indicate that UGT84B1 plays an important role in IAA and PAA homeostasis in Arabidopsis.

    GH3 Auxin-Amido Synthetases Alter the Ratio of Indole-3-Acetic Acid and Phenylacetic Acid in Arabidopsis
    Aoi, Yuki ; Tanaka, Keita ; Cook, Sam David ; Hayashi, Ken Ichiro ; Kasahara, Hiroyuki - \ 2020
    Plant and Cell Physiology 61 (2020)3. - ISSN 0032-0781 - p. 596 - 605.
    Arabidopsis - Auxin - Biosynthesis - Inactivation - Indole-3-acetic acid - Phenylacetic acid

    Auxin is the first discovered plant hormone and is essential for many aspects of plant growth and development. Indole-3-acetic acid (IAA) is the main auxin and plays pivotal roles in intercellular communication through polar auxin transport. Phenylacetic acid (PAA) is another natural auxin that does not show polar movement. Although a wide range of species have been shown to produce PAA, its biosynthesis, inactivation and physiological significance in plants are largely unknown. In this study, we demonstrate that overexpression of the CYP79A2 gene, which is involved in benzylglucosinolate synthesis, remarkably increased the levels of PAA and enhanced lateral root formation in Arabidopsis. This coincided with a significant reduction in the levels of IAA. The results from auxin metabolite quantification suggest that the PAA-dependent induction of GRETCHEN HAGEN 3 (GH3) genes, which encode auxin-amido synthetases, promote the inactivation of IAA. Similarly, an increase in IAA synthesis, via the indole-3-acetaldoxime pathway, significantly reduced the levels of PAA. The same adjustment of IAA and PAA levels was also observed by applying each auxin to wild-type plants. These results show that GH3 auxin-amido synthetases can alter the ratio of IAA and PAA in plant growth and development.

    Piece-by-piece analysis of additives and manufacturing byproducts in plastics ingested by seabirds: Implication for risk of exposure to seabirds
    Tanaka, Kosuke ; Franeker, Jan A. van; Deguchi, Tomohiro ; Takada, Hideshige - \ 2019
    Marine Pollution Bulletin 145 (2019). - ISSN 0025-326X - p. 36 - 41.
    marine lastic debris - plastic ingestion - Additive chemicals - Flame retardans - UV stabilizers - Styrene oligomers
    The risk of marine organisms ingesting plastics has become a growing concern due to hazard chemicals in plastics. To identify compounds to which seabirds potentially have substantial exposure, 194 plastics fragments and pellets ingested by seabirds, i.e., northern fulmars from the Faroe Islands, and laysan albatross and blackfooted albatross from Mukojima Island, were analyzed piece by piece. Four kinds of UV stabilizers, 2 brominated flame retardants, and styrene oligomers were detected at detection frequencies of 4.6%, 2.1%, and 2.1%, respectively. Concentrations ranging from not detected (n.d.) – 1700 μg/g were measured for UV stabilizers, n.d. – 1100 μg/g for flame retardants, and n.d. – 3200 μg/g for styrene oligomers. We found that these chemicals could
    be retained in plastics during drifting and fragmentation in the ocean and transported to seabirds. This type of transport via plastics can be direct pathway that introduces hazardous compounds to marine organisms.
    Hazardous Chemicals in Plastics in Marine Environments : International Pellet Watch
    Yamashita, Rei ; Tanaka, Kosuke ; Yeo, Bee Geok ; Takada, Hideshige ; Franeker, Jan A. van; Dalton, Megan ; Dale, Eric - \ 2019
    In: Hazardous Chemicals Associated with Plastics in the Marine Environment Springer Verlag (Handbook of Environmental Chemistry ) - ISBN 9783319955667 - p. 163 - 183.
    Additives - Equilibrium - Open ocean - Pellets - Sorption

    Marine plastic debris, including microplastics <5Â mm, contain additives as well as hydrophobic chemicals sorbed from surrounding seawater. A volunteer-based global monitoring programme entitled International Pellet Watch (IPW) is utilizing the sorptive nature of plastics, more specifically of beached polyethylene (PE) pellets, in order to measure persistent organic pollutants (POPs) throughout the world. Spatial patterns of polychlorinated biphenyls (PCBs) and organochlorine pesticides have been revealed. Original data of IPW show large piece-to-piece variability in PCB concentrations in pellets collected at each location. This is explained by the combination of slow sorption/desorption and large variabilities of speed and route of floating plastics. The sporadically high concentrations of POPs, both sorbed chemicals and hydrophobic additives, are frequently observed in pellets and the other microplastics in open ocean and remote islands. This poses a chemical threat to marine ecosystems in remote areas.

    Determining sectoral and regional sensitivity to climate and socio-economic change in Europe using impact response surfaces
    Fronzek, Stefan ; Carter, Timothy R. ; Pirttioja, Nina ; Alkemade, Rob ; Audsley, Eric ; Bugmann, Harald ; Flörke, Martina ; Holman, Ian ; Honda, Yasushi ; Ito, Akihiko ; Janes-Bassett, Victoria ; Lafond, Valentine ; Leemans, Rik ; Mokrech, Marc ; Nunez, Sarahi ; Sandars, Daniel ; Snell, Rebecca ; Takahashi, Kiyoshi ; Tanaka, Akemi ; Wimmer, Florian ; Yoshikawa, Minoru - \ 2019
    Regional Environmental Change 19 (2019)3. - ISSN 1436-3798 - p. 679 - 693.
    Gross domestic product (GDP) - Impact model - Population - Precipitation - Sensitivity analysis - Temperature

    Responses to future changes in climatic and socio-economic conditions can be expected to vary between sectors and regions, reflecting differential sensitivity to these highly uncertain factors. A sensitivity analysis was conducted using a suite of impact models (for health, agriculture, biodiversity, land use, floods and forestry) across Europe with respect to changes in key climate and socio-economic variables. Depending on the indicators, aggregated grid or indicative site results are reported for eight rectangular sub-regions that together span Europe from northern Finland to southern Spain and from western Ireland to the Baltic States and eastern Mediterranean, each plotted as scenario-neutral impact response surfaces (IRSs). These depict the modelled behaviour of an impact variable in response to changes in two key explanatory variables. To our knowledge, this is the first time the IRS approach has been applied to changes in socio-economic drivers and over such large regions. The British Isles region showed the smallest sensitivity to both temperature and precipitation, whereas Central Europe showed the strongest responses to temperature and Eastern Europe to precipitation. Across the regions, sensitivity to temperature was lowest for the two indicators of river discharge and highest for Norway spruce productivity. Sensitivity to precipitation was lowest for intensive agricultural land use, maize and potato yields and Scots pine productivity, and highest for Norway spruce productivity. Under future climate projections, North-eastern Europe showed increases in yields of all crops and productivity of all tree species, whereas Central and East Europe showed declines. River discharge indicators and forest productivity (except Holm oak) were projected to decline over southern European regions. Responses were more sensitive to socio-economic than to climate drivers for some impact indicators, as demonstrated for heat-related mortality, coastal flooding and land use.

    Differences in infectivity and pathogenicity of two Plantago asiatica mosaic virus isolates in lilies
    Tanaka, Masashi ; Verbeek, Martin ; Takehara, Miki ; Pham, Khanh ; Lemmers, Miriam ; Slootweg, Casper ; Arie, Tsutomu ; Komatsu, Ken - \ 2019
    European Journal of Plant Pathology 153 (2019)3. - ISSN 0929-1873 - p. 813 - 823.
    Environmental effects - Infectivity - Necrosis - Ornamental lily - Pathogenicity - Plantago asiatica mosaic virus

    Plantago asiatica mosaic virus (PlAMV) is a member of the genus Potexvirus in the family Alphaflexiviridae and has been isolated from a variety of host plants. In particular, PlAMV isolates from ornamental lilies (Lilium spp.) cause necrotic symptoms in these plants, which significantly reduces their commercial value. However, it has not been clear whether PlAMV isolates from other host plants differ in their infectivity and/or pathogenicity to ornamental lilies, and whether growth conditions affect infectivity and pathogenicity. In this study, we inoculated an edible lily species (Lilium leichtlinii) and seven varieties of ornamental lilies with two PlAMV isolates, an isolate from ornamental lily (PlAMV-OL) and an isolate from edible lily (PlAMV-Li1). We found that PlAMV-OL showed higher infection rates and exhibited necrotic symptoms more frequently in lilies than PlAMV-Li1. Moreover, we observed higher infection rates of PlAMV-OL in open field than in greenhouse, and higher rates of necrotic symptoms in autumn test than in spring test, suggesting that growth conditions and season affect infectivity and pathogenicity of PlAMV in lilies. Our study would provide important information for estimating the risk of necrotic disease caused by PlAMV, as well as for cultivation management preventing the occurrence of the disease.

    BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-golgi network/early endosome in arabidopsis thaliana
    Kitakura, Saeko ; Adamowski, Maciek ; Matsuura, Yuki ; Santuari, Luca ; Kouno, Hirotaka ; Arima, Kohei ; Hardtke, Christian S. ; Friml, Jiř ; Kakimoto, Tatsuo ; Tanaka, Hirokazu - \ 2017
    Plant and Cell Physiology 58 (2017)10. - ISSN 0032-0781 - p. 1801 - 1811.
    Arabidopsis - ARF GEF - Auxin - Brefeldin A - PIN-FORMED1 - Trans-Golgi network

    Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to the fungal toxin brefeldin A (BFA), which is known to inhibit guanine nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been fully revealed. In a previous study, we identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. BEN3/BIG2 tagged with fluorescent proteins co-localized with markers for the TGN/early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA sensitive, and established BEN3/BIG2 as a crucial component of this BFA action at the level of the TGN/EE. Furthermore, ben3 mutation alleviated BFAinduced agglomeration of another TGN-localized ARF GEF, BEN1/MIN7. Taken together, our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.

    Erratum to : Performance evaluation of operational atmospheric correction algorithms over the East China Seas (Chinese Journal of Oceanology and Limnology, (2017), 35, 1, (1-22), 10.1007/s00343-016-5170-6)
    He, Shuangyan ; He, Mingxia ; Fischer, Jürgen ; Yuan, Dongliang ; Xu, Peng ; Xu, Tengfei ; Yang, Xianping ; Sokoletsky, Leonid ; Wei, Xiaodao ; Shen, Fang ; Zou, Juhong ; Guo, Maohua ; Cui, Songxue ; Zhou, Wu ; Gao, Dalu ; Jin, Guangzhen ; Lü, Xianqing ; Qiu, Fuwen ; Fang, Wendong ; Pan, Aijun ; Cha, Jing ; Zhang, Shanwu ; Huang, Jiang ; Wang, Tao ; Cheng, Yongzhou ; Chen, Xiaoyan ; Liu, Zhaopu ; Long, Xiaohua ; Hou, Zhishuai ; Wen, Haishen ; Li, Jifang ; He, Feng ; Liu, Qun ; Wang, Jinhuan ; Guan, Biao ; Wang, Qinglong ; Shahjahan, Md ; Kabir, Md Farajul ; Sumon, Kizar Ahmed ; Bhowmik, Lipi Rani ; Rashid, Harunur ; Li, Shu ; Yu, Kefu ; Zhao, Jianxin ; Feng, Yuexing ; Chen, Tianran ; Zhou, Shun ; Ren, Yichao ; Pearce, Christopher M. ; Dong, Shuanglin ; Tian, Xiangli ; Gao, Qinfeng ; Wang, Fang ; Liu, Liming ; Du, Rongbin ; Zhang, Xiaoling ; Dong, Shuanglin ; Sun, Shichun ; Feng, Song ; Lin, Jianing ; Sun, Song ; Zhang, Fang ; Zhang, Zhipeng ; Tang, Xuexi ; Tang, Haitian ; Song, Jingjing ; Zhou, Jian ; Liu, Hongjun ; Wang, Qixiang ; Qian, Kuimei ; Liu, Xia ; Chen, Yuwei ; Sun, Chengjun ; Jiang, Fenghua ; Gao, Wei ; Li, Xiaoyun ; Yu, Yanzhen ; Yin, Xiaofei ; Wang, Yong ; Ding, Haibing ; Sun, Zhongmin ; Wang, Yongqiang ; Yan, Pengcheng ; Guo, Hui ; Yao, Jianting ; Tanaka, Jiro ; Kawai, Hiroshi ; Song, Na ; Chen, Muyan ; Gao, Tianxiang ; Yanagimoto, Takashi ; Lu, Xia ; Luan, Sheng ; Kong, Jie ; Hu, Longyang ; Mao, Yong ; Zhong, Shengping ; Liu, Yan ; Zhao, Weihong ; Li, Caiyan ; Miao, Hui - \ 2017
    Chinese Journal of Oceanology and Limnology 35 (2017)2. - ISSN 0254-4059 - p. 466 - 467.
    Unfortunately for all articles of Vol. 35 No. 1 the future journal title “Journal of Oceanology and Limnology” was used instead of the current journal title “Chinese Journal of Oceanology and Limnology”. All articles in the issue are aff ected. Please make sure to cite the articles with the following Vol. and No. info: Chinese Journal of Oceanology and Limnology, Vol. 35 No. 1, [page range].
    Associations between common variants in iron-related genes with haematological traits in populations of African ancestry
    Gichohi-Wainaina, W.N. ; Tanaka, T. ; Towers, Wayne ; Verhoef, J.C.M. ; Veenemans, J. ; Talsma, E.F. ; Harryvan, J.L. ; Boekschoten, M.V. ; Feskens, E.J.M. ; Melse-Boonstra, A. - \ 2016
    PLoS ONE 11 (2016)6. - ISSN 1932-6203 - 17 p.
    BackgroundLarge genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations.MethodsWe tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels.ResultsIn the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only.ConclusionsIn all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations.
    Assessment of rice self-sufficiency in 2025 in eight African countries
    Oort, P.A.J. van; Saito, K. ; Tanaka, A. ; Amovin-Assagaba, E. ; Bussel, L.G.J. van; Wart, J. van; Groot, H.L.E. de; Ittersum, M.K. van; Cassman, K.G. ; Wopereis, M.C.S. - \ 2015
    Global Food Security 5 (2015). - ISSN 2211-9124 - p. 39 - 49.
    Most African countries are far from self-sufficient in meeting their rice consumption; in eight countries the production: consumption ratio, ranged from 0.16 to 1.18 in 2012. We show that for the year 2025, with population growth, diet change and yield increase on existing land (intensification), countries cannot become fully self-sufficient in rice. This implies that for the future, a mixture of area expansion and imports will be needed on top of yield gap closure. Further research is needed for identification of most suitable new land for rice area expansion and areas that should be protected.
    Interactive teaching and experience extraction for learning about objects and robot activities
    Lim, Gi Hyun ; Oliveira, Miguel ; Mokhtari, Vahid ; Kasaei, S.H. ; Chauhan, Aneesh ; Lopes, Luis Seabra ; Tome, Ana Maria - \ 2014
    In: The 23rd IEEE International Symposium on Robot and Human Interactive Communication. - IEEE - ISBN 9781479967636 - p. 153 - 160.

    Intelligent service robots should be able to improve their knowledge from accumulated experiences through continuous interaction with the environment, and in particular with humans. A human user may guide the process of experience acquisition, teaching new concepts, or correcting insufficient or erroneous concepts through interaction. This paper reports on work towards interactive learning of objects and robot activities in an incremental and open-ended way. In particular, this paper addresses human-robot interaction and experience gathering. The robot's ontology is extended with concepts for representing human-robot interactions as well as the experiences of the robot. The human-robot interaction ontology includes not only instructor teaching activities but also robot activities to support appropriate feedback from the robot. Two simplified interfaces are implemented for the different types of instructions including the teach instruction, which triggers the robot to extract experiences. These experiences, both in the robot activity domain and in the perceptual domain, are extracted and stored in memory, and they are used as input for learning methods. The functionalities described above are completely integrated in a robot architecture, and are demonstrated in a PR2 robot.

    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Molecular dynamics simulation of energy migration between tryptophan residues in apoflavodoxin
    Nunthaboot, N. ; Tanaka, F. ; Kokpol, S. ; Visser, N.V. ; Amerongen, H. van; Visser, A.J.W.G. - \ 2014
    RSC Advances : An international journal to further the chemical sciences 4 (2014). - ISSN 2046-2069 - p. 31443 - 31451.
    time-resolved fluorescence - azotobacter-vinelandii - anisotropy decay - force-field - flavodoxin - proteins - water - pathway - system - state
    Molecular dynamics (MD) simulations over a 30 ns trajectory have been carried out on apoflavodoxin from Azotobacter vinelandii to compare with the published, experimental time-resolved fluorescence anisotropy results of F¨orster Resonance Energy Transfer (FRET) between the three tryptophan residues. MD analysis of atomic coordinates yielding both the time course of geometric parameters and the time-correlated second-order Legendre polynomial functions reflects immobilization of tryptophans in the protein matrix. However, one tryptophan residue (Trp167) undergoes flip-flop motion on the nanosecond timescale. The simulated time-resolved fluorescence anisotropy of tryptophan residues in apoflavodoxin implying a model of two unidirectional FRET pathways is in very good agreement with the experimental time-resolved fluorescence anisotropy, although the less efficient FRET pathway cannot be resolved and is hidden in the contribution of a slow protein motion.
    Evaluation of using spot urine to replace 24 h urine sodium and potassium excretions
    Hooft Van Huysduynen, E.J.C. ; Hulshof, P.J.M. ; Lee, L. van; Geelen, A. ; Feskens, E.J.M. ; Veer, P. van 't; Woerkum, C.M.J. van; Vries, J.H.M. de - \ 2014
    Public Health Nutrition 17 (2014)11. - ISSN 1368-9800 - p. 2505 - 2511.
    24-hour - collections - completeness - creatinine - magnesium - calcium - samples - marker - acid
    Objective The most accurate method to estimate Na and K intakes is to determine 24 h urinary excretions of these minerals. However, collecting 24 h urine is burdensome. Therefore it was studied whether spot urine could be used to replace 24 h urine samples. Design Participants collected 24 h urine and kept one voiding sample separate. Na, K and creatinine concentrations were analysed in both 24 h and spot urine samples. Also 24 h excretions of Na and K were predicted from spot urine concentrations using the Tanaka and Danish methods. Setting In 2011 and 2012, urine samples were collected and brought to the study centre at Wageningen University, the Netherlands. Subjects Women (n 147) aged 19–26 years. Results According to p-aminobenzoic acid excretions, 127 urine collections were complete. Correlations of Na:creatinine, K:creatinine and Na:K between spot urine and 24 h urine were 0·68, 0·57 and 0·64, respectively. Mean 24 h Na excretion predicted with the Tanaka method was higher (difference 21·2 mmol/d, P
    Mother-to-Infant Transmission of Intestinal Bifidobacterial Strains Has an Impact on the Early Development of Vaginally Delivered Infant's Microbiota
    Makino, H. ; Kushiro, A. ; Ishikawa, E. ; Kubota, H. ; Gawad, A. ; Sakai, T. ; Oishi, K. ; Martin, R. ; Ben-Amor, K. ; Knol, J. ; Tanaka, R. - \ 2013
    PLoS ONE 8 (2013)11. - ISSN 1932-6203
    species-specific primers - milk oligosaccharides - gut microbiota - fecal flora - bacterial - microflora - colonization - diversity - identification - sequence
    Objectives: Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine. Materials and Methods: Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5). Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium), 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR. Results: Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age. Conclusions: Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.
    Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease
    Meurs, J.B.J. van; Pare, G. ; Schwartz, S.M. ; Hazra, A. ; Tanaka, T. ; Vermeulen, S.H. ; Cotlarciuc, I. ; Yuan, X. ; Malarstig, A. ; Bandinelli, S. ; Bis, J.C. ; Morn, H. ; Brown, M.J. ; Chen, C. ; Chen, Y.D. ; Clarke, R.J. ; Dehghan, A. ; Erdmann, J. ; Ferrucci, L. ; Hamsten, A. ; Hofman, A. ; Hunten, D.J. ; Goel, A. ; Johnson, A.D. ; Kathiresan, S. ; Kampman, E. ; Kiel, D.P. ; Kiemeney, L.A. ; Chambers, J.C. ; Kraft, P. ; Lindemans, J. ; McKnight, B. ; Nelson, C.P. ; O'Donnell, C.J. ; Psaty, B.M. ; Ridken, P.M. ; Rivadeneira, F. ; Rose, L.M. ; Seedoif, U. ; Siscovick, D.S. ; Schunkert, H. ; Selhub, J. ; Ueland, P.M. ; Vollenweiden, P. ; Waeben, G. ; Waterworth, D.M. ; Watkins, H. ; Witteman, J.C.M. ; Heijen, M. den; Jacques, P. ; Uitterlinden, A.G. ; Koonet, J.S. ; Rader, D.J. ; Reilly, M.P. ; Moose, V. ; Chasman, D.I. ; Samani, N.J. ; Ahmadi, K.R. - \ 2013
    American Journal of Clinical Nutrition 98 (2013)3. - ISSN 0002-9165 - p. 668 - 676.
    genome-wide association - cardiovascular-disease - mendelian randomization - heart-disease - expression - metaanalysis - mthfr - polymorphism - women - identification
    Background: The strong observational association between total homocysteine (tHcy) concentrations and risk of coronary artery disease (CAD) and the null associations in the homocysteinelowering trials have prompted the need to identify genetic variants associated with homocysteine concentrations and risk of CAD. Objective: We tested whether common genetic polymorphisms associated with variation in tlicy are also associated with CAD. Design: We conducted a meta-analysis of genome-wide association studies (GWAS) on tHcy concentrations in 44,147 individuals of European descent. Polymolphisms associated with tHcy (P <10(-8)) were tested for association with CAD in 31,400 cases and 92,927 controls. Results: Common variants at 13 loci, explaining 5.9% of the variation in tHcy, were associated with tHcy concentrations, including 6 novel loci in or near MMACHC (2.1 X 10(-9)), SLC17A3 (1.0 x 10(-8)), GTPB10 (1.7 X 10(-8)), CUBN (7.5 X 10(-1)), HNFlA (1.2 x 10(-12)), and FUT2 (6.6 x 10(-9)), and variants previously reported at or near the MTHFR, MTR, CPS1, MUT, NOX4, DPEP1, and CBS genes. Individuals within the highest 10% of the genotype risk score (GRS) had 3-gmol/L higher mean tHcy concentrations than did those within the lowest 10% of the GRS (P = 1 X 10(-36)). The GRS was not associated with risk of CAD (OR: 1.01; 95% CI: 0.98, 1.04; P = 0.49). Conclusions: We identified several novel loci that influence plasma tHcy concentrations. Overall, common genetic variants that influence plasma tHcy concentrations are not associated with risk of CAD in white populations, which further refutes the causal relevance of moderately elevated tHey concentrations and tHcy-related pathways for CAD.
    Families of Dothideomycetes
    Hyde, K.D. ; Gareth Jones, E.B. ; Liu, J.K. ; Ariyawansa, H. ; Boehm, E. ; Boonmee, S. ; Braun, U. ; Chomnunti, P. ; Crous, P.W. ; Dai, D.Q. ; Diederich, P. ; Dissanayake, A. ; Doilom, M. ; Doveri, F. ; Hongsanan, S. ; Jayawardena, R. ; Lawrey, J.D. ; Li, Y.M. ; Liu, Y.X. ; Lücking, R. ; Monkai, J. ; Muggia, L. ; Nelsen, M.P. ; Pang, K.L. ; Phookamsak, R. ; Senanayake, I.C. ; Shearer, C.A. ; Suetrong, S. ; Tanaka, K. ; Thambugala, K.M. ; Wijayawardene, N.N. ; Wikee, S. ; Wu, H.X. ; Zhang, Y. ; Aguirre-Hudson, B. ; Alias, S.A. ; Aptroot, A. ; Bahkali, A.H. ; Berezza, J.L. ; Bhat, D.J. ; Camporesi, E. ; Chukeatirote, E. ; Gueidan, C. ; Hawksworth, D.L. ; Hirayama, K. ; Hoog, S. de; Kang, J.C. ; Knudsen, K. ; Li, W.J. ; Li, X.H. ; Liu, Z.Y. ; Mapook, A. ; McKenzie, E.H.C. ; Miller, A.N. ; Mortimer, P.E. ; Phillips, A.J.L. ; Raja, H.A. ; Scheuer, C. ; Schumm, F. ; Taylor, J.E. ; Tian, Q. ; Tibpromma, S. ; Wanasinghe, D.N. ; Wang, Y. ; Xu, J.C. ; Yacharoen, S. ; Yan, J.Y. ; Zhang, M. - \ 2013
    Fungal Diversity 63 (2013)1. - ISSN 1560-2745 - p. 1 - 313.
    ribosomal dna-sequences - morphologically similar genera - foliicolous lichenized fungi - intertidal mangrove wood - leaf-inhabiting fungi - fresh-water habitats - new-zealand fungi - russian far-east - papua-new-guinea - sp-nov
    Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.
    Global inventory of closed-off Tidal basins and developments after the closure
    Schultz, B. ; Hayde, L.G. ; Sang-Hyun, P. ; Tanaka, K. - \ 2013
    Irrigation and Drainage 62 (2013)Suppl. 1. - ISSN 1531-0353 - p. 107 - 123.
    porous ceramic cups - deep drainage - clay soil - tillage - nitrate - vertosols - systems
    Closed-off tidal basin reclamation represents a special type of reclamation. In several countries enclosing dams have been built to close off estuaries, shallow seas, or lagoons, and lands up to 5~6¿m - MSL (below mean sea level) have been reclaimed in the former tidal basins. Although these areas were generally primarily reclaimed for agriculture, a second-stage development may have taken place where parts of these lands were transferred to urban and industrial use. The originally saline water in the created reservoirs was transformed to fresh water that may be used for irrigation, domestic and/or industrial water supply. In several of these reservoirs there are water quality problems, primarily due to pollution in upstream parts of the river basins. In 2007 the Enclosing Dam of the Zuiderzee Scheme in the Netherlands had existed for 75¿years. This occasion was used to conduct a global inventory of closed-off tidal basin reclamation on which this paper is based. The study shows that closed-off tidal basin reclamation concerns 25 schemes with a total area of 738 000¿ha, of which 337 000¿ha have been reclaimed and 401 000¿ha freshwater reservoirs have been created. This paper presents a summarized overview. Attention is paid to safety, land use and changes in it, development of water quality in the reservoirs, as well as to land subsidence and possible impacts of climate change, like rise in mean sea level. In time this may have implications for safety of the deep polders, the management of the reservoirs as well as for the sustainable development of tidal areas in the future. These items are presented for four major tidal reclamation schemes: the Zuiderzee Scheme in the Netherlands, the Saemangeum Scheme in South Korea, the Kuttanad Region in India and the Hachirogata Scheme in Japan
    Intrinsic inter- and intraspecific competition in parasitoid wasps
    Harvey, J.A. ; Poelman, E.H. ; Tanaka, T. - \ 2013
    Annual Review of Entomology 58 (2013). - ISSN 0066-4170 - p. 333 - 351.
    lepidoptera larvae compete - interspecific competition - heliothis-virescens - endoparasitoid wasps - insect parasitoids - biological-control - heteronomous hyperparasitoids - gregarious development - campoletis-sonorensis - microplitis-croceipes
    Immature development of parasitoid wasps is restricted to resources found in a single host that is often similar in size to the adult parasitoid. When two or more parasitoids of the same or different species attack the same host, there is competition for monopolization of host resources. The success of intrinsic competition differs between parasitoids attacking growing hosts and parasitoids attacking paralyzed hosts. Furthermore, the evolution of gregarious development in parasitoids reflects differences in various developmental and behavioral traits, as these influence antagonistic encounters among immature parasitoids. Fitness-related costs (or benefits) of competition for the winning parasitoid reveal that time lags between successive attacks influence the outcome of competition. Physiological mechanisms used to exclude competitors include physical and biochemical factors that originate with the ovipositing female wasp or her progeny. In a broader multitrophic framework, indirect factors, such as plant quality, may affect parasitoids through effects on immunity and nutrition.
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