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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    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.
    Intrinsic competition among solitary and gregarious endoparasitoid wasps and the phenomenon of ‘resource sharing’
    Magdaraog, P.M. ; Harvey, J.A. ; Tanaka, T. ; Gols, R. - \ 2012
    Ecological Entomology 37 (2012)1. - ISSN 0307-6946 - p. 65 - 74.
    intraspecific larval competition - interspecific competition - meteorus-pulchricornis - developmental interactions - hymenoptera-braconidae - insect multiparasitism - microplitis-demolitor - copidosoma-floridanum - pseudaletia-separata - heliothis-virescens
    1. Intrinsic competition was compared in three species of braconid wasps, the solitary Meteorus pulchricornis Wesmael, and the gregarious Cotesia kariyai (Watanabe) and Cotesia ruficrus Haliday in caterpillars of their common host, the armyworm Mythimna separata Walker. Competition was determined in pair-wise contests consisting of simultaneous and subsequent parasitisms at various time intervals between the first and second attacks (
    Additions to the Mycosphaerella complex
    Crous, P.W. ; Tanaka, K. ; Summerell, B.A. ; Groenewald, J.Z. - \ 2011
    IMA fungus 2 (2011)1. - ISSN 2210-6340 - p. 49 - 64.
    Species in the present study were compared based on their morphology, growth characteristics in culture, and DNA sequences of the nuclear ribosomal RNA gene operon (including ITS1, ITS2, 5.8S nrDNA and the first 900 bp of the 28S nrDNA) for all species and partial actin and translation elongation factor 1-alpha gene sequences for Cladosporium species. New species of Mycosphaerel/a (Mycosphaerel/aceae) introduced in this study include M. cerastiicola (on Cerastium semidecandrum, The Netherlands), and M. etlingerae (on Etlingera e/atior, Hawaii). Mycosphaerel/a holualoana is newly reported on Hedychium coronarium (Hawaii). Epitypes are also designated for Hendersonia persooniae, the basionym of Camarosporula persooniae, and for Sphaerel/a agapanthi, the basionym of Teratosphaeria agapanthi comb. nov. (Teratosphaeriaceae) on Agapathus umbel/atus from South Africa. The latter pathogen is also newly recorded from A. umbel/atus in Europe (Portugal). Furthermore, two sexual species of Cladosporium (Davidiel/aceae) are described, namely C. grevil/eae (on Grevil/ea sp., Australia), and C. silenes (on Silene maritima, UK). Finally, the phylogenetic position of two genera are newly confirmed, namely Camarosporula (based on C. persooniae, teleomorph Anthracostroma persooniae), which is a leaf pathogen of Persoonia spp. in Australia, belongs to the Teratosphaeriaceae, and Sphaerulina (based on S. myriadea), which occurs on leaves of Fagaceae (Carpinus, Castanopsis, Fagus, Quercus), and belongs to the Mycosphaerel/aceae.
    Differing Success of Defense Strategies in Two Parasitoid Wasps in Protecting Their Pupae Against a Secondary Hyperparasitoid
    Harvey, J.A. ; Gols, R. ; Tanaka, T. - \ 2011
    Annals of the Entomological Society Of America 104 (2011)5. - ISSN 0013-8746 - p. 1005 - 1011.
    cotesia-glomerata l. - meteorus-pulchricornis - behavioral manipulation - separata lepidoptera - pseudaletia-separata - insect parasitoids - host caterpillars - life-history - braconidae - hymenoptera
    During their larval development, endoparasitoids are known to dispose of host resources in several different ways. Some parasitoid wasps consume most or all tissues of the host, whereas others consume a small fraction of host resources and either ensure that the host moves away from the pupation site or allow the host to remain close to the parasitoid cocoon(s). Using a single host species, Mythimna separata Walker (Lepidoptera: Noctuidae), this study compares the success of the two pupation strategies in the solitary parasitoids Microplitis sp. and Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae) against attack from a secondary hyperparasitoid, Gelis agilis F. (Hymenoptera: Ichneumonidae). The caudal appendages of M. separata caterpillars parasitized by Microplitis sp. remain physically attached to parasitoid cocoons and the caterpillars behave aggressively when disturbed. However, after Me. pulchricornis larvae emerge from caterpillars of their host, M. separata, the parasitoid larvae pupate in cocoons that are suspended by a single thick thread that hangs 1–2 cm from under a leaf. In choice tests conducted in petri dishes, significantly fewer cocoons of Microplitis sp. attended by caterpillars than unattended cocoons were hyperparasitized by G. agilis. By contrast, Me. pulchricornis cocoons that were hanging from corn, Zea mays L., plants were hyperparasitized as frequently as those which were attached to leaves. We discuss the potentially different selection pressures generated among natural enemies such as predators and hyperparasitoids in determining optimal pupal defense strategies in primary parasitoids.
    The ‘usurpation hypothesis’ revisited: dying caterpillar repels attack from a hyperparasitoid wasp
    Harvey, J.A. ; Tanaka, T. ; Kruidhof, M. ; Vet, L.E.M. ; Gols, R. - \ 2011
    Animal Behaviour 81 (2011)6. - ISSN 0003-3472 - p. 1281 - 1287.
    cotesia-glomerata l. - host behavior - developmental strategies - hymenoptera-braconidae - apanteles-melanoscelus - southwestern virginia - pseudaletia-separata - manipulation - parasitoids - lepidoptera
    It has been posited that some parasitoid wasps ‘usurp’ their dying hosts as ‘bodyguards’ to protect the vulnerable parasitoid cocoons against attack from natural enemies such as predators or hyperparasitoids. Thus far, however, the hypothesis has been supported only in studies with insect predators. Two factors may account for this: first, hyperparasitoids, being more specialized than predators, are probably less easily rebuffed by the presence of an attending caterpillar; second, the host cocoon is used for reproduction by hyperparasitoids, but not by predators. We compared the survival of a solitary primary parasitoid, Microplitis sp., and successful parasitism by a secondary hyperparasitoid, Gelis agilis, from parasitoid cocoons with and without the presence of an ‘attending’ larva of the host, the armyworm, Mythimna separata. Mature Microplitis sp. larvae always emerge through the same host segment, leaving the posterior segments paralysed and attached to cocoons and the anterior segments freely moving. When disturbed by G. agilis females, M. separata larvae exhibited aggressive behaviour that repeatedly drove off approaching hyperparasitoids. In choice and no-choice experiments performed at 24 h intervals over 96 h, G. agilis successfully parasitized cocoons without attending caterpillars, but few cocoons with attending caterpillars were ever parasitized. Choice experiments, in which G. agilis wasps were released onto corn plants containing 24 h-old parasitoid cocoons with and without attending caterpillars, produced similar results. We provide the first experimental evidence that a solitary parasitoid usurps the behaviour of its host over several days as a ‘bodyguard’ against hyperparasitoids
    Overall welfare assessment of laying hens: Comparing science-based, environmental-based and animal-based assessments
    Shimmura, T. ; Bracke, M.B.M. ; Mol, R.M. de; Hirahara, S. ; Tanaka, T. - \ 2011
    Animal Science journal 82 (2011)1. - ISSN 1344-3941 - p. 150 - 160.
    decision-support system - burmese red junglefowl - large furnished cages - housing systems - domestic hens - feather pecking - battery cages - dustbathing behavior - rearing environment - physical condition
    To increase the validity of evaluations and facilitate expansion and maintenance of assessment systems, we constructed a database of studies on the welfare of laying hens around the world. On the basis of this database, we devised a science-based welfare assessment model. Our model includes measurements, levels and weightings based on the scientific studies in the database, and can clarify the advantages and disadvantages of housing systems for laying hens from the viewpoint of the five freedoms. We also evaluated the usefulness of our model by comparing it with environment-based Animal Needs Index (ANI), another science-based model called FOWEL, and animal-based measurements. Our model showed that freedom from injury, pain and disease, and freedom from discomfort were more secure in the cage system, while non-cage systems scored better for natural behavior and freedom from fear and distress. A significant strong-positive correlation was found between the animal-based assessment and the total scores of ANI (rs = 0.94, P <0.05), FOWEL (rs = 0.99, P <0.05) or our model (rs = 0.99, P <0.05), which indicate that these different approaches to welfare assessment may be used almost interchangeably to ‘measure’ a common property (‘overall laying hen welfare’). However, assessments using our model and FOWEL were more sensitive than ANI and can be applied to cage systems, which suggest that our model and FOWEL may have added value.
    Functional and evolutionary insights from the genomes of three parasitoid nasonia species
    Werren, John H. ; Richards, Stephen ; Desjardins, Christopher A. ; Niehuis, Oliver ; Gadau, Jurgen ; Colbourne, John K. ; Beukeboom, Leo W. ; Desplan, Claude ; Elsik, Christine G. ; Grimmelikhuijzen, Cornelis J.P. ; Kitts, Paul ; Lynch, Jeremy A. ; Murphy, Terence ; Oliveira, Deodoro C.S.G. ; Smith, Christopher D. ; Zande, Louis De Van; Worley, Kim C. ; Zdobnov, Evgeny M. ; Aerts, Maarten ; Albert, Stefan ; Anaya, Victor H. ; Anzola, Juan M. ; Barchuk, Angel R. ; Behura, Susanta K. ; Bera, Agata N. ; Berenbaum, May R. ; Bertossa, Rinaldo C. ; Bitondi, Márcia M.G. ; Bordenstein, Seth R. ; Bork, Peer ; Bornberg-Bauer, Erich ; Brunain, Marleen ; Cazzamali, Giuseppe ; Chaboub, Lesley ; Chacko, Joseph ; Chavez, Dean ; Childers, Christopher P. ; Choi, Jeong Hyeon ; Clark, Michael E. ; Claudianos, Charles ; Clinton, Rochelle A. ; Cree, Andrew G. ; Cristino, Alexandre S. ; Dang, Phat M. ; Darby, Alistair C. ; Graaf, Dirk C. De; Devreese, Bart ; Dinh, Huyen H. ; Edwards, Rachel ; Elango, Navin ; Elhaik, Eran ; Ermolaeva, Olga ; Evans, Jay D. ; Foret, Sylvain ; Fowler, Gerald R. ; Gerlach, Daniel ; Gibson, Joshua D. ; Gilbert, Donald G. ; Graur, Dan ; Gründer, Stefan ; Hagen, Darren E. ; Han, Yi ; Hauser, Frank ; Hultmark, Da ; Hunter Iv, Henry C. ; Hurst, Gregory D.D. ; Jhangian, Shalini N. ; Jiang, Huaiyang ; Johnson, Reed M. ; Jones, Andrew K. ; Junier, Thomas ; Kadowaki, Tatsuhiko ; Kamping, Albert ; Kapustin, Yuri ; Kechavarzi, Bobak ; Kim, Jaebum ; Kim, Jay ; Kiryutin, Boris ; Koevoets, Tosca ; Kovar, Christie L. ; Kriventseva, Evgenia V. ; Kucharski, Robert ; Lee, Heewook ; Lee, Sandra L. ; Lees, Kristin ; Lewis, Lora R. ; Loehlin, David W. ; Logsdon, John M. ; Lopez, Jacqueline A. ; Lozado, Ryan J. ; Maglott, Donna ; Maleszka, Ryszard ; Mayampurath, Anoop ; Mazur, Danielle J. ; McClure, Marcella A. ; Moore, Andrew D. ; Morgan, Margaret B. ; Muller, Jean ; Munoz-Torres, Monica C. ; Muzny, Donna M. ; Nazareth, Lynne V. ; Neupert, Susanne ; Nguyen, Ngoc B. ; Nunes, Francis M.F. ; Oakeshott, John G. ; Okwuonu, Geoffrey O. ; Pannebakker, Bart A. ; Pejaver, Vikas R. ; Peng, Zuogang ; Pratt, Stephen C. ; Predel, Reinhard ; Pu, Ling Ling ; Ranson, Hilary ; Raychoudhury, Rhitoban ; Rechtsteiner, Andreas ; Reese, Justin T. ; Reid, Jeffrey G. ; Riddle, Megan ; Robertson, I.I.H.M. ; Romero-Severson, Jeanne ; Rosenberg, Miriam ; Sackton, Timothy B. ; Sattelle, David B. ; Schlüns, Helge ; Schmitt, Thomas ; Schneider, Martina ; Schüler, Andreas ; Schurko, Andrew M. ; Shuker, David M. ; Simões, Zila L.P. ; Sinha, Saurabh ; Smith, Zachary ; Solovyev, Victor ; Souvorov, Alexandre ; Springauf, Andreas ; Stafflinger, Elisabeth ; Stage, Deborah E. ; Stanke, Mario ; Tanaka, Yoshiaki ; Telschow, Arndt ; Vattathil, Carol Trent Selina ; Verhulst, I.I.E.C. ; Viljakainen, Lumi ; Wanner, Kevin W. ; Waterhouse, Robert M. ; Whitfield, James B. ; Wilkes, Timothy E. ; Williamson, Michael ; Willis, Judith H. ; Wolschin, Florian ; Wyder, Stefan ; Yamada, Takuji ; Yi, Soojin V. ; Zecher, Courtney N. ; Zhang, Lan ; Gibbs, Richard A. - \ 2010
    Science 327 (2010)5963. - ISSN 0036-8075 - p. 343 - 348.

    We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. tongicomis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-spedfic genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclearmitochondrial interactions that are implicated in spedation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.

    Bioavailability of Xenobiotics in the Soil Environment
    Katayama, A. ; Bhula, R. ; Burns, G.R. ; Carazo, E. ; Felsot, A. ; Hamilton, D. ; Harris, C. ; Kim, Y.H. ; Kleter, G.A. ; Koedel, W. ; Linders, J. ; Peijnenburg, J.G.M.W. ; Sabljic, A. ; Stephenson, R.G. ; Racke, D.K. ; Rubin, B. ; Tanaka, K. ; Unsworth, J. ; Wauchope, R.D. - \ 2010
    In: Reviews of Environmental Contamination and Toxicology, Vol. 203 / Whitacre, D.M., New York : Springer - ISBN 9781441913517 - p. 1 - 86.
    polycyclic aromatic-hydrocarbons - supercritical-fluid extraction - bound pesticide-residues - field-moist soils - artificially contaminated soils - persistent organic pollutants - earthworms eisenia-foetida - carbon-dioxide extraction - bacterial outer-membrane
    When synthetic, xenobiotic compounds such as agrochemicals and industrial chemicals are utilized, they eventually reach the soil environment where they are subject to degradation, leaching, volatilization, sorption, and uptake by organisms. The simplest assumption is that such chemicals in soil are totally available to microorganisms, plant roots, and soil fauna via direct, contact exposure; subsequently these organisms are consumed as part of food web processes and bioaccumulation may occur, increasing exposures to higher organisms up the food chain. However, studies in the last two decades have revealed that chemical residues in the environment are not completely bioavailable, so that their uptake by biota is less than the total amount present in soil (Alexander 1995; Gevao et al. 2003; Paine et al. 1996). Therefore, the toxicity, biodegradability, and efficacy of xenobiotics are dependent on their soil bioavailability, rendering this concept profoundly important to chemical risk assessment and pesticide registration.
    Electrostatic potentials of humic acid: Fluorescence quenching measurements and comparison with model calculations
    Saito, T. ; Koopal, L.K. ; Nagasaki, S. ; Tanaka, S. - \ 2009
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 347 (2009)1-3. - ISSN 0927-7757 - p. 27 - 32.
    natural organic-matter - nica-donnan model - ion-binding - charge adjustments - proton binding - substances - adsorption - system - soft
    Average electrostatic potentials of purified Aldrich humic acid (PAHA) are measured, based on quenching of the PAHA fluorescence by neutral and cationic quencher molecules with similar structures. The obtained negative potentials increased with increasing pH at a given salt concentration and weakly decreased with increasing salt concentration at given pH. The trends and the magnitudes of the potentials correspond with the few experimental results available in the literature. Comparison with potentials calculated by the electrostatic models from the charge of PAHA revealed that the average potentials obtained from the ion permeable sphere model and Donnan-EDL model agreed with the measured average potentials. With these two models it is assumed that a part of the PAHA charge is neutralized by the electrical double layer (EDL) around the PAHA particle in line with the view that humic acid is a nano-size particle partly permeable to small ions and solvent molecules. The potentials calculated by these two models are averages of the potential "inside" the particle (which governs the proton binding) and that in the EDL. The Donnan models, with both the fixed charges and the counter charges distributed over a volume that is greater than the particle volume itself, result in more negative potentials than the measured average potentials of PAHA. These observations suggest that the quenchers are located close to the functional groups but diffusely bound.
    Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
    Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
    ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
    Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
    A class-wide phylogenetic assessment of Dothideomycetes
    Schoch, C.L. ; Crous, P.W. ; Groenewald, J.Z. ; Boehm, E.W.A. ; Burgess, T.I. ; Gruyter, J. de; Hoog, G.S. de; Dixon, L.J. ; Grube, M. ; Gueidan, C. ; Harada, Y. ; Hatakeyama, S. ; Hirayama, K. ; Hosoya, T. ; Huhndorf, S.M. ; Hyde, K.D. ; Jones, E.B.G. ; Kohlmeyer, J. ; Kruys, Å. ; Li, Y.M. ; Lücking, R. ; Lumbsch, H.T. ; Marvanová, L. ; Mbatchou, J.S. ; McVay, A.H. ; Miller, A.N. ; Mugambi, G.K. ; Muggia, L. ; Nelsen, M.P. ; Nelson, P. ; Owensby, C.A. ; Phillips, A.J.L. ; Phongpaichit, S. ; Pointing, S.B. ; Pujade-Renaud, V. ; Raja, H.A. ; Rivas Plata, E. ; Robbertse, B. ; Ruibal, C. ; Sakayaroj, J. ; Sano, T. ; Selbmann, L. ; Shearer, C.A. ; Shirouzu, T. ; Slippers, B. ; Suetrong, S. ; Tanaka, K. ; Volkmann-Kohlmeyer, B. ; Wingfield, M.J. ; Wood, A.R. ; Woudenberg, J.H.C. ; Yonezawa, H. ; Zhang, Y. ; Spatafora, J.W. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 1 - 15.
    ribosomal dna-sequences - multigene phylogenies - molecular phylogeny - maximum-likelihood - multiple alignment - marine ascomycota - rdna sequences - fungi - evolution - classification
    We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon
    Adsorption of heterogeneously charged nanoparticles on a variably charged surface by the extended surface complexation approach: Charge regulation, chemical heterogeneity, and surface complexation
    Saito, T. ; Koopal, L.K. ; Nagasaki, S. ; Tanaka, S. - \ 2008
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 112 (2008)5. - ISSN 1520-6106 - p. 1339 - 1349.
    spherical colloidal particles - double-layer interaction - electrical double-layer - electrostatic free-energy - poisson-boltzmann theory - natural organic-matter - humic substances - polyelectrolyte adsorption - protein adsorption - ion-binding
    Adsorption of randomly branched polyelectrolytes, hairy particles and internally structured macromolecules, collectively denoted as heterogeneously charged nanoparticles, on charged surfaces is important in. many technological and natural processes. In this paper, we will focus on (1) the charge regulation of both the nanoparticle and the surface and (2) the surface complexation between the particle functional groups and the surface sites and will theoretically study the adsorption using the extended surface complexation approach. The model explicitly considers the electrochemical potential of a nanoparticle with an average (smeared-out) structure and charge both in bulk solution and on the surface to obtain the equilibrium adsorption. The chemical heterogeneity of the particle is described by a distribution of the protonation constant. Detailed analysis of the chemical potential of the adsorbed nanoparticle reveals that the pH and salt dependence of the adsorption can be largely explained by the balance between an energy gain resulting from the particle and surface charge regulation and the surface complexation and an energy loss from the unfavorable interparticle electrostatic repulsion close to the surface. This conclusion is also supported by the strong impacts that the chemical heterogeneity of the particle functional groups, the magnitude of the surface complexation, the number of the functional groups, and the size of the particle have on the adsorption.
    Interannual variation of water balance and summer evapotranspiration in an eastern Siberian larch forest over a 7-year period (1998-2006)
    Ohta, T. ; Maximov, T.C. ; Dolman, A.J. ; Nakai, T. ; Molen, M.K. van der; Kononov, A.V. ; Maximov, T. ; Hiyama, T. ; Iijima, Y. ; Moors, E.J. ; Tanaka, H. - \ 2008
    Agricultural and Forest Meteorology 148 (2008)12. - ISSN 0168-1923 - p. 1941 - 1953.
    surface-energy balance - boreal aspen forest - long-term - vegetation - exchange - fluxes - carbon - transpiration - conductance - closure
    Water vapor, energy fluxes, and environmental conditions were measured in an eastern Siberian larch forest for 7 water years, from 1998 to 2006, to understand the water-balance characteristics and interannual variation (IAV). The latent heat flux accounted for 38¿67% of the sum of turbulent heat fluxes in June, July, and August, a relatively moderate fraction was compared to values measured at mid- and low latitudes. More than 70% of the annual precipitation evaporated during May to September. Annual evapotranspiration, including interception loss, was relatively steady at 169¿220 mm compared with the wide range in annual precipitation (111¿347 mm year¿1). The evapotranspiration rate was 1.49¿2.30 mm day¿1 on a daily basis from May to September above a dry canopy. This feature is one of the remarkable characteristics of the water balance in eastern Siberian forests. The thawing depth of the permafrost has been rapidly deepening since 2004, such that the maximal thawing depth varied from 127 cm before 2003 to over 200 cm after 2004. At the same time, there was a very large increase in the moisture content of the surface soil. This increase could not be explained by the amount of annual precipitation alone and may have been due to inflow from the deeper thawing layer. The IAV of evapotranspiration was small, but the yearly evapotranspiration coefficient (the ratio of evapotranspiration to potential evaporation) ranged from 0.30 to 0.45. These results indicate that the IAV of evapotranspiration is controlled by regulation of the land surface rather than by atmospheric demand. Soil-moisture content was the most important variable among the factors determining the evapotranspiration coefficient at an interannual temporal scale. This result differs somewhat from previous satellite-based findings that air temperature was a major variable for plant activity. This difference might result from the fact that the IAV of soil water content did not correspond to that of the precipitation amount because of the presence of the permafrost. By contrast, the soil water content was strongly affected by precipitation in the previous summer.
    Comparing the physiological effects and function of larval feeding in closely-related endoparasitoids (Braconidae: Microgastrinae)
    Harvey, J.A. ; Bezemer, T.M. ; Gols, R. ; Nakamatsu, Y. ; Tanaka, T. - \ 2008
    Physiological Entomology 33 (2008)3. - ISSN 0307-6962 - p. 217 - 225.
    wasp cotesia-congregata - hornworm manduca-sexta - 4 trophic levels - tobacco hornworm - parasitic wasp - developmental strategies - insect parasitoids - host behavior - growth - hymenoptera
    The larvae of most endoparasitoid wasps consume virtually all host tissues before pupation. However, in some clades, the parasitoid larvae primarily consume haemolymph and fat body and emerge through the side of the host, which remains alive and active for up to several days. The evolutionary significance of this host-usage strategy has attracted attention in recent years. Recent empirical studies suggest that the surviving larva guards the parasitoid broods against natural enemies such as predators and hyperparasitoids. Known as the 'usurpation hypothesis', the surviving larvae bite, regurgitate fluids from the gut, and thrash the head capsule when disturbed. In the present study, the 'usurpation hypothesis' is tested in the association involving Manduca sexta, its parasitoid Cotesia congregata, and a secondary hyperparasitoid Lysibia nana. Percentage parasitoid survival is higher and hyperparasitism lower when cocoons of C. congregata are attached to the dorsum of M. sexta caterpillars. Fat body contents in several associations involving solitary and gregarious parasitoids feeding on haemolymph and fat body are also compared. The amount of fat body retained in parasitized caterpillars varies considerably from one association to another. In M. sexta and Pieris brassicae, considerable amounts of fat body remain after parasitoid emergence whereas, in Cotesia kariyai and Cotesia rufricus, virtually all of the fat body is consumed by the parsasitoid larvae. The length of post-egression survival of parasitized caterpillars differs considerably in several tested associations. In Pseudeletia separata, most larvae die within a few hours of parasitoid emergence whereas, in M. sexta, parasitized larvae live up to 2 weeks after parasitoid emergence. Larvae in other associations parasitized by gregarious and solitary endoparasitoids live for intermediate periods. The results are discussed in relation to the adaptive significance of different feeding strategies of immature parasitoids and of the costs and benefits of retaining the parasitized caterpillar in close proximity with the parasitoid cocoons
    Do Parasitized caterpillars protect their parasitoids from hyperparasitoids? A test of the 'usurpation hypothesis'
    Harvey, J.A. ; Kos, M. ; Nakamatsu, Y. ; Tanaka, T. ; Dicke, M. ; Vet, L.E.M. ; Brodeur, J. ; Bezemer, T.M. - \ 2008
    Animal Behaviour 76 (2008)3. - ISSN 0003-3472 - p. 701 - 708.
    host behavior - insect parasitoids - wasp - manipulation - braconidae - predation - selection - quality - snail - larva
    Caterpillars that are attacked by some species of parasitoid wasps are known to survive for several days after the parasitoid larvae emerge and pupate. It has been argued that the behaviour of the parasitized larva is `usurped¿ by the parasitoid and that it `guards¿ the parasitoid cocoons against their own natural enemies such as hyperparasitoids (the `usurpation hypothesis'). We tested this hypothesis in the association involving a gregarious endoparasitoid, the wasp Cotesia glomerata; caterpillars of its host, the large cabbage white butterfly Pieris brassicae; and a pupal hyperparasitoid, the wasp Lysibia nana. In laboratory experiments, we presented cocoon broods of C. glomerata to single females of L. nana in arenas for 6 h. We tested several treatments for rates of primary parasitoid survival, including variation in the position of the caterpillar and the presence or absence of an additional silk web spun by parasitized caterpillars. Parasitized P. brassicae larvae survived longer than the period necessary for C. glomerata adults to emerge. Rates of parasitoid survival were, however, unaffected by the presence of a P. brassicae larva on the cocoon brood, although significantly more parasitoids emerged when the silk web was present. Analyses of the foraging behaviour of individual L. nana females in arenas, performed using Observer software, revealed that the wasps showed a greater tendency to leave cocoons when caterpillars and silk were present. The laboratory experiments only partially support the usurpation hypothesis. In nature, usurpation of the host of the primary parasitoid may be a more effective strategy against generalist predators than against more specialized and better-adapted hyperparasitoids
    Trends in Pesticide Use on Transgenic versus Conventional Crops
    Kleter, G.A. ; Bhula, R. ; Bodnaruk, K. ; Carazo, E. ; Felsot, A.S. ; Harris, C.A. ; Katayama, A. ; Kuiper, H.A. ; Racke, K.D. ; Rubin, B. ; Shevah, Y. ; Stephenson, G.R. ; Tanaka, K. ; Unsworth, J. ; Wauchope, R.D. ; Wong, S.S. - \ 2008
    ISB News Report 2008 (2008)8. - p. 5 - 8.
    Altered pesticide use on transgenic crops and the associated general impact from an environmental perspective
    Kleter, G.A. ; Bhula, R. ; Bodnaruk, K. ; Carazo, E. ; Felsot, A.S. ; Harris, C.A. ; Katayama, A. ; Kuiper, H.A. ; Racke, K.D. ; Rubin, B. ; Shevah, Y. ; Stephenson, G.R. ; Tanaka, K. ; Unsworth, J. ; Wauchope, R.D. ; Wong, S.S. - \ 2007
    Pest Management Science 63 (2007)11. - ISSN 1526-498X - p. 1107 - 1115.
    farm-level - cotton - india
    The large-scale commercial cultivation of transgenic crops has undergone a steady increase since their introduction 10 years ago. Most of these crops bear introduced traits that are of agronomic importance, such as herbicide or insect resistance. These traits are likely to impact upon the use of pesticides on these crops, as well as the pesticide market as a whole. Organizations like USDA-ERS and NCFAP monitor the changes in crop pest management associated with the adoption of transgenic crops. As part of an IUPAC project on this topic, recent data are reviewed regarding the alterations in pesticide use that have been observed in practice. Most results indicate a decrease in the amounts of active ingredients applied to transgenic crops compared with conventional crops. In addition, a generic environmental indicator - the environmental impact quotient (EIQ) - has been applied by these authors and others to estimate the environmental consequences of the altered pesticide use on transgenic crops. The results show that the predicted environmental impact decreases in transgenic crops. With the advent of new types of agronomic trait and crops that have been genetically modified, it is useful to take also their potential environmental impacts into account.
    Analysis of copper binding in the ternary system Cu2+/Humic Acid/Goethite at neutral to acidic pH
    Saito, T. ; Koopal, L.K. ; Nagasaki, S. ; Tanaka, S. - \ 2005
    Environmental Science and Technology 39 (2005)13. - ISSN 0013-936X - p. 4886 - 4893.
    metal-ion binding - adsorbed humic substances - natural organic-matter - competitive adsorption - exchange properties - charge adjustments - exafs spectroscopy - fulvic-acid - goethite - model
    Binding of heavy metal and actinide ions to natural colloids, such as humic substances (HSs) and metal (hydr)oxides, plays an important role in the ecotoxicological behavior of these ions. Several thermodynamic models have been constructed to predict the speciation of these ions in metal/HS or metal/oxide binary systems. However, in natural environments the adsorption of HSs on oxides can influence the binding of target metals, leading to deviation from the additivity of calibrated binary models. In this study binding of copper (Cu 2+) to the purified Aldrich humic acid (PAHA)/goethite complex in the neutral to acidic pH region was investigated by measuring Cu2+ binding isotherms. The measured isotherms were compared with the results obtained for the binary systems under similar conditions. The comparison revealed that Cu2+ binding in the ternary system is enhanced with respect to the sum of Cu2+ binding in the corresponding binary systems. From the analysis of the charging behavior of the adsorbed PAHA as well as the smeared-out potential profile near the PAHA/goethite interface, the increase of Cu2+ binding to the complex was mainly attributed to the decrease of proton competition to the functional groups of the adsorbed PAHA and the change of the electrostatic potential in the vicinity of the goethite surface
    The effect of the cultivation of genetically modified crops on the use of pesticides and the impact thereof on the environment
    Kleter, G.A. ; Bhula, R. ; Bodnaruk, K. ; Carazo, E. ; Felsot, A.S. ; Harris, C.A. ; Katayama, A. ; Kuiper, H.A. ; Racke, K. ; Rubin, B. ; Shevah, Y. ; Stephenson, G.R. ; Tanaka, K. ; Unsworth, J. ; Wong, S.S. - \ 2005
    In: International workshop on crop protection chemistry in Latin America : harmonized approaches for environmental assessment and regulation 14 - 17 February, 2005, San Jose, Costa Rica Oxford : IUPAC - p. 49 - 76.
    Electrostatic interaction models for ion binding to humic substances
    Saito, T. ; Nagasaki, S. ; Tanaka, S. ; Koopal, L.K. - \ 2005
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 265 (2005)1-3. - ISSN 0927-7757 - p. 104 - 113.
    proton binding - chemical-composition - molecular-size - acids - parameters - adsorption - matter
    Preferably, the description of ion binding to humic substances (HSs) is done with thermodynamic constants that do not depend on the environmental conditions. To solve this problem, models have to be made that describe the electrostatic and specific interactions. With a given electrostatic model the charge/pH curves of HS at different salt levels can be re-plotted as a function of the local pH near the sites (pHloc) of HSs. If the model is appropriate, the charge/pHloc curves will merge into a master curve (MC). In this study five electrostatic models were investigated to obtain pHloc for purified Aldrich humic acid (PAHA): rigid sphere (RS), ion-permeable sphere, Donnan (NICA), Donnan-EV, and Donnan-EDL. The RS model is tested in two versions; one based on the measured hydrodynamic radius (RS-a h) and the other on an optimized radius (RS-aopt). The ion-permeable sphere model uses the hydrodynamic radius and provides the potential distribution; as characteristic potential the radial average inside the sphere is used. In the Donnan (NICA) model the volume of the sphere, V D, in which the charge of PAHA is neutralized, is optimized with a constraint between VD and ionic strength, and in the Donnan-EV model VD is calculated by setting the radius of the gel as the sum of the hydrodynamic radius of PAHA and the Debye length. The Donnan-EDL model uses the hydrodynamic particle radius and is based on a combination of the Donnan model and the diffuse electrical double layer model. Only the RS-aopt, Donnan (NICA), and Donnan-EV models give adequate MCs. The positions of the MCs differ with respect to each other. This means that the discrimination between electrostatic and intrinsic interactions is model-dependent and therefore arbitrary. The Donnan (NICA) model has a practical advantage over the other two models because this model needs no measurements of the size of HS. For the purpose of the routine fitting of ion-binding data to an ion-binding isotherm equation that includes the electrostatics, this advantage is quite important
    Application of the NICADonnan model for proton, copper and uranyl binding to humic acid
    Saito, T. ; Nagasaki, S. ; Tanaka, S. ; Koopal, L.K. - \ 2004
    Radiochimica Acta 92 (2004)9-11. - ISSN 0033-8230 - p. 567 - 574.
    metal-ion binding - fulvic-acids - humate interactions - substances - complexation - adsorption - parameters - heterogeneity - uranium(vi) - goethite
    Humic acids are natural organic materials that play an important role in the migration of heavy metal and actinide ions in aquatic and soil systems. In the present study, the binding of protons, copper ions and uranyl ions to the purified Aldrich humic acid (PAHA) is investigated and the results are modeled with the Non-Ideal Competitive Adsorption (NICA) model extended with electrostatic interactions according to the Donnan model (NICA-Donnan model). The NICA part of the model enables one to describe the competitive ion binding to a heterogeneous substrate taking into account a different stoichiometry per ion. The NICA-Donnan model can describe the binding of the ions to PAHA in large concentration ranges (3
    Adsorption of humic acid on goethite: Isotherms, charge adjustments and potential profiles
    Saito, T. ; Koopal, L.K. ; Riemsdijk, W.H. van; Nagasaki, S. ; Tanaka, S. - \ 2004
    Langmuir 20 (2004)3. - ISSN 0743-7463 - p. 689 - 700.
    natural organic-matter - oxide-water interface - metal-ion binding - donnan model parameters - fulvic-acid - iron-oxide - polyelectrolyte adsorption - weak polyelectrolytes - humate interactions - surface ionization
    The adsorption of natural organic matter (NOM) on mineral (hydr)oxide plays an important role in the evaluation of the speciation of toxic metal ions in the environment. Because both NOM and mineral oxide have variable charges that adjust upon adsorption, a good understanding of proton binding is required before the binding of metal ions can be understood. In this study, the adsorption of purified Aldrich humic acid (PAHA) on goethite was examined as a function of the environmental conditions (pH, salt concentration, and free concentration of PAHA) together with the proton adsorption to PAHA, goethite, and their mixtures. The induced charges on both components were separated on the basis of the difference between the charge/pH curves of the mixture and those of the single components. The electrostatic potential profile across the adsorbed layer was obtained as a numerical solution of the Poisson-Boltzmann equation using the charge density of the adsorbed PAHA and the goethite surface. From the quantitative evaluation of the induced charge on both components, it is revealed that the degree of the charge adjustment is related to the electrostatic affinity between the PAHA segments and the goethite surface, the electrostatic repulsion between the PAHA segments, and the electrostatic shielding by salt ions. Considering the charge distribution of the adsorbed PAHA at the goethite surface, it is concluded that the change of the charge adjustment is sensitive to that of the conformation of the adsorbed PAHA. From the detailed inspection of the assumptions made and the comparison with the reported theoretical calculations, the obtained potential profiles are considered to broadly reflect the true potential profiles. Because a charge adjustment is not frequently considered in detail in relation to the NOM adsorption on metal (hydr)oxides, the obtained results can form the basis for the further development of modeling of the adsorption of NOM on (hydr)oxide surfaces.
    Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics
    Tolstikov, V.V. ; Lommen, A. ; Nakanishi, K. ; Tanaka, N. ; Fiehn, O. - \ 2003
    Analytical Chemistry 75 (2003)23. - ISSN 0003-2700 - p. 6737 - 6740.
    functional genomics - polar compounds - ionization - columns - identification - validation - efficiency - flavonoids
    Application of C18 monolithic silica capillary columns in HPLC coupled to ion trap mass spectrometry detection was studied for probing the metabolome of the model plant Arabidopsis thaliana. It could be shown that the use of a long capillary column is an easy and effective approach to reduce ionization suppression by enhanced chromatographic resolution. Several hundred peaks could be detected using a 90-cm capillary column for LC separation and a noise reduction and automatic peak alignment software, which outperformed manual inspection or commercially available mass spectral deconvolution software.
    The stacked flavin adenine dinucleotide conformation in water is fluorescent on picosecond timescale.
    Chosrowjan, H. ; Taniguchi, S. ; Mataga, N. ; Tanaka, F. ; Visser, A.J.W.G. - \ 2003
    Chemical Physics Letters 378 (2003). - ISSN 0009-2614 - p. 354 - 358.
    time-resolved fluorescence - nuclear magnetic-resonance - protein nanospace - electron-transfer - dynamics - flavoproteins - spectroscopy - chromophores - proton
    The fluorescence upconversion technique has been applied to examine the picosecond fluorescence decay kinetics of flavin adenine dinucleotide (FAD) in aqueous solution. In the observation range of 30 ps three fluorescent lifetimes can be distinguished. The shortest-lived component (similar to1 ps) arises from water relaxation around the excited flavin. The 9-ps component originates from the intramolecular complex between flavin and adenine, whereas the nanosecond decay is attributed to the unstacked form of FAD. The spectra of the three forms are derived from global analysis of decay curves at different emission wavelengths and time regimes using a triple exponential function. It is assumed that the amplitude belonging to the nanosecond fluorescence component reflects the steady-state fluorescence spectrum. Fluorescence anisotropy to its maximum value of 0.4 is instantaneously created. (C) 2003 Elsevier B.V. All rights reserved.
    Binding site of novel 2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine herbicides in the D1 protein of Photosystem II
    Ikeda, Y. ; Ohki, S. ; Koizumi, K. ; Tanaka, A. ; Watanabe, H. ; Kohno, H. ; Rensen, J.J.S. van; Böger, P. ; Wakabayashi, K. - \ 2003
    Photosynthesis Research 77 (2003). - ISSN 0166-8595 - p. 35 - 43.
    photosynthetic electron-transport - chloroplasts - inhibition - derivatives - resistant
    A series of replacement experiments of [C-14]-triazines, [C-14]-atrazine and [7-C-14]-2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine, bound to thylakoids isolated from wild-type and atrazine-resistant Chenopodium album (lambsquarters) were conducted. Replacement experiments of [C-14]-triazines bound to wild-type Chenopodium thylakoids with non-labeled atrazine and 2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine were carried out, to elucidate whether benzylamino-1,3,5-triazines use the same binding niche as atrazine. [C-14]-Atrazine and [7-C-14]-2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine bound to wild-type thylakoids were replaced by non-labeled 2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine and non-labeled atrazine, respectively. The above two replacements showed mutual competition. To clarify further whether benzylamino-1,3,5-triazines bind at the D1-protein to amino acid residue( s) different from atrazine or not, experiments to replace [7-C-14]-2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazines bound to atrazine-resistant Chenopodium thylakoids by non-labeled atrazine, 2-(4-bromobenzylamino)-4-methyl-6-trifluoromethyl-1,3,5-triazine, DCMU and DNOC were carried out. Although the bound [7-C-14]-2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine was difficult to be replaced even with high concentrations of atrazine, [C-14]-labeled 1,3,5-triazine was competitively replaced by non-labeled 2-(4-bromobenzylamino)-4-methyl-6-trifluoromethyl-1,3,5-triazine, DCMU or DNOC. Thus, 2-benzylamino-4-methyl-6-trifluoromethyl-1,3,5-triazine herbicides are considered to bind to the same niche at the D1 protein as atrazine, but use amino acid residue(s) different from those involved with atrazine binding.
    A transcriptional activator, AoXlnR, controls the expression of genes encoding xylanolytic enzymes in Aspergillus oryzae
    Marui, J. ; Tanaka, A. ; Mimura, S. ; Graaff, L.H. de; Visser, J. ; Kitamoto, N. ; Kato, M. ; Kobayashi, T. ; Tsukagoshi, N. - \ 2002
    Fungal Genetics and Biology 35 (2002)2. - ISSN 1087-1845 - p. 157 - 169.
    taka-amylase-a - zinc binuclear cluster - shoyu koji mold - molecular-cloning - escherichia-coli - sequence-analysis - beta-xylosidase - reductase gene - xylanase genes - amino-acid
    By deletion across the promoter region of the xynF1 gene encoding the major Aspergillus oryzae xylanase, a 53-bp DNA fragment containing the XlnR binding sequence GGCTAAA as well as two similar sequences was shown to confer xylan inducibility on the gene. Complementary and genomic DNAs encoding the Aspergillus niger xlnR homologous gene, abbreviated AoxlnR, were cloned from A. oryzae and sequenced. AoXlnR comprised 971 amino acids with a zinc binuclear cluster domain at the N-terminal region and revealed 77.5% identity to the A. niger XlnR. Recombinant AoXlnR protein encompassing the zinc cluster region of the N-terminal part bound to both the consensus binding sequence and its cognate sequence, GGCTGA, with an approximately 10 times lower affinity. GGCTA/GA is more appropriate as the XlnR consensus binding sequence. Both sequences functioned independently in vivo in XlnR-mediating induction of the xynF1 gene. This was further confirmed by using an AoxlnR disruptant. Neither the xynF1 nor the xylA gene was expressed in the disruptant, suggesting that the xylan-inducible genes in A. oryzae may also be controlled in the same manner as described for A. niger
    Treatment of waste activated sludge by thermophylic acidifying UASB reactor
    Tanaka, Y. ; Sanders, W.T.M. ; Zeeman, G. - \ 1999
    Japanese Journal of Water Treatment Biology 35 (1999)1. - p. 9 - 18.
    Light climate and growth in shade-tolerant Fagus crenata, Acer mono and Carpinus cordata.
    Peters, R. ; Hiroshi Tanaka, ; Mitsue Shibata, ; Tohru Nakashizuka, - \ 1995
    Ecoscience 2 (1995). - ISSN 1195-6860 - p. 67 - 74.
    The effect of high temperature in long days on the floral induction of the short-day plant, Perilla crispa (Thunp.) Tanaka.
    Wellensiek, S.J. - \ 1987
    Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen. Serie C: Biological and medical sciences 90 (1987). - ISSN 0023-3374 - p. 231 - 238.
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