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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    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Computational metabolomics to characterize metabolites in stable isotope-labeled organisms
    Tsugawa, H. ; Nakabayashi, R. ; T., Mori ; Yamada, Y. ; Takahashi, M. ; Rai, A. ; Sugiyama, R. ; Yamamoto, H. ; Nakaya, T. ; Yamazaki, M. ; Kooke, R. ; Molenaar, J.A. ; Oztolan-Erol, N. ; Keurentjes, J.J.B. ; Arita, M. ; Saito, K. - \ 2019
    Journal of the American Society for Mass Spectrometry 30 (2019)supplement 1. - ISSN 1044-0305 - p. 163 - 163.
    Cruise report of multidisciplinary ecosystem survey in the eastern Indian sector of the Antarctic (CCAMLR Division 58.4.1) with a focus on Antarctic krill during 2018/19 season by the Japanese survey vessel, Kaiyo-maru.
    Murase, H. ; Abe, K. ; Matsukura, R. ; Sasaki, H. ; Driscoll, R. ; Driscoll, S. ; Schaafsma, F.L. ; Regteren, M. van; Yang, Q. ; Ohshima, H. ; Ohshima, K. ; Sugioka, R. ; Tong, J. ; Yamamoto, N. ; Doiguchi, H. ; Briggs, E. ; Doi, K. ; Hirano, D. ; Katsumata, K. ; Kiuchi, M. ; Ko, Y. ; Nomura, D. ; Orui, M. ; Sato, H. ; Toyoda, S. ; Yamazaki, K. ; Ishihara, T. ; Hamabe, K. ; Kumagai, S. ; Miyashita, T. ; Yamada, N. ; Koyama, Y. ; Sasaki, H. - \ 2019
    Convention for the Conservation of Antarctic Marine Living Resources CCAMLR
    Publisher Correction: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms
    Tsugawa, Hiroshi ; Nakabayashi, Ryo ; Mori, Tetsuya ; Yamada, Yutaka ; Takahashi, Mikiko ; Rai, Amit ; Sugiyama, Ryosuke ; Yamamoto, Hiroyuki ; Nakaya, Taiki ; Yamazaki, Mami ; Kooke, Rik ; Bac-Molenaar, Johanna A. ; Oztolan-Erol, Nihal ; Keurentjes, Joost J.B. ; Arita, Masanori ; Saito, Kazuki - \ 2019
    Nature Methods : techniques for life scientists and chemists 16 (2019)5. - ISSN 1548-7091 - p. 446 - 446.

    In the originally published Supplementary Information for this paper, the files presented as Supplementary Tables 3, 4, and 7 were duplicates of Supplementary Tables 5, 6, and 9, respectively. All Supplementary Table files are now correct online.

    A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms
    Tsugawa, Hiroshi ; Nakabayashi, Ryo ; Mori, Tetsuya ; Yamada, Yutaka ; Takahashi, Mikiko ; Rai, Amit ; Sugiyama, Ryosuke ; Yamamoto, Hiroyuki ; Nakaya, Taiki ; Yamazaki, Mami ; Kooke, Rik ; Bac-Molenaar, Johanna A. ; Oztolan-Erol, Nihal ; Keurentjes, Joost J.B. ; Arita, Masanori ; Saito, Kazuki - \ 2019
    Nature Methods : techniques for life scientists and chemists 16 (2019)4. - ISSN 1548-7091 - p. 295 - 298.

    We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13 C-labeled and non-labeled plants and LC–MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.

    Implementation of non-local boundary layer schemes in the Regional Atmospheric Modeling System and its impact on simulated mesoscale circulations
    Gómez, I. ; Ronda, R.J. ; Caselles, V. ; Estrela, M.J. - \ 2016
    Atmospheric Research 180 (2016). - ISSN 0169-8095 - p. 24 - 41.
    Boundary layer - Mesoscale modelling - Non-local schemes - Numerical weather prediction/forecasting - PBL parameterization - RAMS model

    This paper proposes the implementation of different non-local Planetary Boundary Layer schemes within the Regional Atmospheric Modeling System (RAMS) model. The two selected PBL parameterizations are the Medium-Range Forecast (MRF) PBL and its updated version, known as the Yonsei University (YSU) PBL. YSU is a first-order scheme that uses non-local eddy diffusivity coefficients to compute turbulent fluxes. It is based on the MRF, and improves it with an explicit treatment of the entrainment. With the aim of evaluating the RAMS results for these PBL parameterizations, a series of numerical simulations have been performed and contrasted with the results obtained using the Mellor and Yamada (MY) scheme, also widely used, and the standard PBL scheme in the RAMS model. The numerical study carried out here is focused on mesoscale circulation events during the summer, as these meteorological situations dominate this season of the year in the Western Mediterranean coast. In addition, the sensitivity of these PBL parameterizations to the initial soil moisture content is also evaluated. The results show a warmer and moister PBL for the YSU scheme compared to both MRF and MY. The model presents as well a tendency to overestimate the observed temperature and to underestimate the observed humidity, considering all PBL schemes and a low initial soil moisture content. In addition, the bias between the model and the observations is significantly reduced moistening the initial soil moisture of the corresponding run. Thus, varying this parameter has a positive effect and improves the simulated results in relation to the observations. However, there is still a significant overestimation of the wind speed over flatter terrain, independently of the PBL scheme and the initial soil moisture used, even though a different degree of accuracy is reproduced by RAMS taking into account the different sensitivity tests.

    A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem
    Kinoshita, A. ; Hove, C.A. ten; Tabata, R. ; Yamada, M. ; Shimizu, N. ; Ishida, T. ; Yamaguchi, K. ; Shigenobu, S. ; Takebayashi, Y. ; Luchies, J. ; Kobayashi, M. ; Kurata, T. ; Wada, T. ; Seo, M. ; Hasebe, M. ; Blilou, I. ; Fukuda, H. ; Scheres, B. ; Heidstra, R. ; Kamiya, Y. ; Sawa, S. - \ 2015
    Development 142 (2015). - ISSN 0950-1991 - p. 444 - 453.
    receptor-like kinase - arabidopsis shoot meristem - of-function phenotypes - cle peptides - gene-expression - repeat protein - differentiation - thaliana - organization - growth
    The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture.
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Nielsen, H.B. ; Almeida, M. ; Sierakowska Juncker, A. ; Rasmussen, S. ; Li, J. ; Sunagawa, S. ; Plichta, D.R. ; Gautier, L. ; Pedersen, A.G. ; Chatelier, E. Le; Pelletier, E. ; Bonde, I. ; Nielsen, T. ; Manichanh, C. ; Arumugam, M. ; Batto, J.M. ; Quintanilha dos Santos, M.B. ; Blom, N. ; Borruel, N. ; Burgdorf, K.S. ; Boumezbeur, F. ; Casellas, F. ; Doré, J. ; Dworzynski, P. ; Guarner, F. ; Hansen, T. ; Hildebrand, F. ; Kaas, R.S. ; Kennedy, S. ; Kristiansen, K. ; Kultima, J.R. ; Leonard, P. ; Levenez, F. ; Lund, O. ; Moumen, B. ; Paslier, D. Le; Pons, N. ; Pedersen, O. ; Prifti, E. ; Qin, J. ; Raes, J. ; Sørensen, S. ; Tap, J. ; Tims, S. ; Ussery, D.W. ; Yamada, T. ; Jamet, A. ; Mérieux, A. ; Cultrone, A. ; Torrejon, A. ; Quinquis, B. ; Brechot, C. ; Delorme, C. ; M'Rini, C. ; Vos, W.M. de; Maguin, E. ; Varela, E. ; Guedon, E. ; Gwen, F. ; Haimet, F. ; Artiguenave, F. ; Vandemeulebrouck, G. ; Denariaz, G. ; Khaci, G. ; Blottière, H. ; Knol, J. ; Weissenbach, J. ; Hylckama Vlieg, J.E. van; Torben, J. ; Parkhil, J. ; Turner, K. ; Guchte, M. van de; Antolin, M. ; Rescigno, M. ; Kleerebezem, M. ; Derrien, M. ; Galleron, N. ; Sanchez, N. ; Grarup, N. ; Veiga, P. ; Oozeer, R. ; Dervyn, R. ; Layec, S. ; Bruls, T. ; Winogradski, Y. ; Zoetendal, E.G. ; Renault, D. ; Sicheritz-Ponten, ; Bork, P. ; Wang, J. ; Brunak, S. ; Ehrlich, S.D. - \ 2014
    Nature Biotechnology 32 (2014). - ISSN 1087-0156 - p. 822 - 828.
    short read alignment - sequences - systems - algorithms - microbiota - protein - life - sets - tree - tool
    Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
    Richness of human gut microbiome correlates with metabolic markers
    Chatelier, E. Le; Nielsen, T. ; Qin, J. ; Prifti, E. ; Hildebrand, F. ; Falony, G. ; Almeida, M. ; Arumugam, M. ; Batto, J.M. ; Kennedy, S. ; Leonard, P. ; Li, J. ; Burgdorf, K. ; Grarup, N. ; Jorgensen, T. ; Branslund, I. ; Nielsen, H.B. ; Juncker, A.S. ; Bertalan, M. ; Levenez, F. ; Pons, N. ; Rasmussen, S. ; Sunagawa, S. ; Tap, J. ; Tims, S. ; Zoetendal, E.G. ; Brunak, S. ; Clement, K. ; Dore, J. ; Kleerebezem, M. ; Kristiansen, K. ; Renault, P. ; Sicheritz-Ponten, T. ; Vos, W.M. de; Zucker, J.D. ; Raes, J. ; Hansen, T. ; Bork, P. ; Wang, J. ; Ehrlich, S.D. ; Pederson, O. ; Guedon, E. ; Delorme, C. ; Layec, S. ; Khaci, G. ; Guchte, M. van de; Vandemeulebrouck, G. ; Jamet, A. ; Dervyn, R. ; Sanchez, N. ; Maguin, E. ; Haimet, F. ; Winogradski, Y. ; Cultrone, A. ; Leclerc, M. ; Juste, C. ; Blottière, H. ; Pelletier, E. ; LePaslier, D. ; Artiguenave, F. ; Bruls, T. ; Weissenbach, J. ; Turner, K. ; Parkhill, J. ; Antolin, M. ; Manichanh, C. ; Casellas, F. ; Boruel, N. ; Varela, E. ; Torrejon, A. ; Guarner, F. ; Denariaz, G. ; Derrien, M. ; Hylckama Vlieg, J.E.T. van; Veiga, P. ; Oozeer, R. ; Knol, J. ; Rescigno, M. ; Brechot, C. ; M'Rini, C. ; Mérieux, A. ; Yamada, T. - \ 2013
    Nature 500 (2013)7464. - ISSN 0028-0836 - p. 541 - 546.
    body-mass index - diet-induced obesity - insulin-resistance - wide association - reared apart - weight-loss - inflammation - adiposity - disease - twins
    We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
    Exploring the Impact of Land Cover and Topography on Rainfall Maxima in the Netherlands
    Maat, H.W. ter; Moors, E.J. ; Hutjes, R.W.A. ; Holtslag, A.A.M. ; Dolman, A.J. - \ 2013
    Journal of Hydrometeorology 14 (2013)2. - ISSN 1525-755X - p. 524 - 542.
    landgebruik - bossen - neerslag - bodemwater - simulatie - modellen - veluwe - land use - forests - precipitation - soil water - simulation - models - veluwe - climate-change - convective boundary - soil-moisture - surface - model - evaporation - prediction - diffusion - exchange
    The relative contribution of topography and land use on precipitation is analyzed in this paper for a forested area in the Netherlands. This area has an average yearly precipitation sum that can be 75–100 mm higher than the rest of the country. To analyze this contribution, different configurations of land use and topography are fed into a mesoscale model. The authors use the Regional Atmospheric Modeling System (RAMS) coupled with a land surface scheme simulating water vapor, heat, and momentum fluxes [Soil–Water–Atmosphere Plant System–Carbon (SWAPS-C)]. The model simulations are executed for two periods that cover varying large-scale synoptic conditions of summer and winter periods. The output of the experiments leads to the conclusion that the precipitation maximum at the Veluwe is forced by topography and land use. The effect of the forested area on the processes that influence precipitation is smaller in summertime conditions when the precipitation has a convective character. In frontal conditions, the forest has a more pronounced effect on local precipitation through the convergence of moisture. The effect of topography on monthly domain-averaged precipitation around the Veluwe is a 17% increase in the winter and a 10% increase in the summer, which is quite remarkable for topography with a maximum elevation of just above 100 m and moderate steepness. From this study, it appears that the version of RAMS using Mellor–Yamada turbulence parameterization simulates precipitation better in wintertime, but the configuration with the medium-range forecast (MRF) turbulence parameterization improves the simulation of precipitation in convective circumstances.
    Demographic costs of masting for a Bornean rain forest tree species, Scaphium macropodum
    Yamada, T. ; Suzuki, E. ; Zuidema, P.A. - \ 2012
    Tropics : monograph series 21 (2012)1. - ISSN 0917-415X - p. 21 - 32.
    Abstract W485. The Rose Genome Sequence Initiative
    Foucher, F. ; Sakr, S. ; Bendahmane, M. ; Smulders, M.J.M. ; Debener, T. ; Riek, J. de; Torres, A.M. ; Amaya, I. ; Millan, T. ; Zamir, D. ; Sargent, D. ; Nybom, H. ; Atanassov, A. ; Hokanson, S.C. ; Byrne, D. ; Sosinski, B. ; Main, D. ; Bruneau, A. ; Rees, J. ; Matsumoto, S. ; Yamada, K. - \ 2012
    Rose is one of the most economically important ornamental crops worldwide. Rosa sp. is well suited genus to become a model for woody ornamentals for a number of reasons: (i) its relative small genome size (500 Mb), (ii) its well documented genetic history with ploïdy events, (iii) its short life for a woody plant, and (iv) availability of different tools, including transcriptomic tools, genetic maps and genetic transformation protocols. Furthermore, the rose represents an original model for studying some ornamental traits that can not be addressed in other model species such as Arabidopsis. Some of these traits, such recurrent blooming, flower morphogenesis or scent production and emission, are of economic interest. The objective of the Rose Genome Sequence Initiative (http://rosegenome.org) is to obtain a high quality rose genome sequence of the diploid R. chinensis ‘Old Blush’. One important issue is the high heterozygosity of roses. To tackle the heterozygosity issue, we propose to develop a high density genetic map to anchor the genome. This genetic map will be developed from a cross between ‘Old Blush’ and R. wichurana. The genotype R. chinensis ‘Old Blush’ will be sequenced using NGS technologies. The data will be assembled and arranged using the high density map. New ESTs will be developed to facilitate assembly and gene annotation. The rose genome sequence will be a great step to help identifying the molecular basis of ornamental traits and also to study genetic diversity and genome evolution in the genus Rosa and in the Rosaceae family.
    Evaluation of the COSMO-SC turbulence scheme in a shear-driven stable boundary layer
    Buzzi, M. ; Rotach, M.W. ; Raschendorfer, M. ; Holtslag, A.A.M. - \ 2011
    Meteorologische Zeitschrift 20 (2011)3. - ISSN 0941-2948 - p. 335 - 350.
    weather prediction model - 2nd-order closure models - low-level jet - intermittent turbulence - surface - flows - land - oscillations - coordinate - stability
    The performance of the COSMOsingle column turbulence scheme (a TKE scheme with a 1.5 order turbulence closure at the hierarchy level 2.5 following Mellor and Yamada) is investigated in the framework of the first GABLS intercomparison case. This is an idealized shear-driven stable boundary layer case with no advection. Overall the COSMO model performs reasonably well compared to the other participating models and the reference Large Eddy Simulations. However, the modification of some model parameters, together with the prescribed high vertical resolution, reveals a problem of numerical stability in the turbulence scheme: for the investigated shear-driven stable boundary layer the vertical diffusivities show unrealistic oscillations. This model deficiency, which has previously been described in literature, is explored in quite substantial detail and possible solutions are evaluated. It is found that under the given conditions the numerical description of the vertical wind gradients is crucial for the stability of the turbulence scheme. It is shown that for the determination of vertical gradients information from grid points beyond the immediately neighboring model levels must be incorporated – as it is common practice in the treatment of horizontal gradients – in order to obtain a numerically stable turbulence scheme. As a first approach vertical wind gradients are filtered using a 5-point filter prior to the evaluation of the stability functions. This approach yields to the overall best performance among all those tested and found in literature. The simulations additionally show that the use of a too high minimum diffusion coefficient (which is introduced in the model in order to avoid too low mixing) leads to losing important structures of the planetary boundary layer, such as the low level jet or a near-surface temperature inversion
    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.

    Relationship between petal abscission and programmed cell death in Prunus yedoensis and Delphinium belladonna
    Yamada, T. ; Ichimura, K. ; Doorn, W.G. van - \ 2007
    Planta 226 (2007)5. - ISSN 0032-0935 - p. 1195 - 1205.
    gene-expression - senescence - flowers - iris - degradation - ethylene - defender - pcd
    Depending on the species, the end of flower life span is characterized by petal wilting or by abscission of petals that are still fully turgid. Wilting at the end of petal life is due to programmed cell death (PCD). It is not known whether the abscission of turgid petals is preceded by PCD. We studied some parameters that indicate PCD: chromatin condensation, a decrease in nuclear diameter, DNA fragmentation, and DNA content per nucleus, using Prunus yedoensis and Delphinium belladonna which both show abscission of turgid petals at the end of floral life. No DNA degradation, no chromatin condensation, and no change in nuclear volume was observed in P. yedoensis petals, prior to abscission. In abscising D. belladonna petals, in contrast, considerable DNA degradation was found, chromatin was condensed and the nuclear volume considerably reduced. Following abscission, the nuclear area in both species drastically increased, and the chromatin became unevenly distributed. Similar chromatin changes were observed after dehydration (24 h at 60°C) of petals severed at the time of flower opening, and in dehydrated petals of Ipomoea nil and Petunia hybrida, severed at the time of flower opening. In these flowers the petal life span is terminated by wilting rather than abscission. It is concluded that the abscission of turgid petals in D. belladonna was preceded by a number of PCD indicators, whereas no such evidence for PCD was found at the time of P. yedoensis petal abscission. Dehydration of the petal cells, after abscission, was associated with a remarkable nuclear morphology which was also found in younger petals subjected to dehydration. This nuclear morphology has apparently not been described previously, for any organism.
    Gene expression in opening and senescing petals of morning glory (Ipomoea nil) flowers
    Yamada, T. ; Ichimura, K. ; Kanekatsu, M. ; Doorn, W.G. van - \ 2007
    Plant Cell Reports 26 (2007)6. - ISSN 0721-7714 - p. 823 - 835.
    programmed cell-death - senescence-associated genes - leaf senescence - arabidopsis-thaliana - cysteine proteinase - postharvest senescence - alstroemeria petals - caffeoyl-coenzyme - identification - disease
    We isolated several senescence-associated genes (SAGs) from the petals of morning glory (Ipomoea nil) flowers, with the aim of furthering our understanding of programmed cell death. Samples were taken from the closed bud stage to advanced visible senescence. Actinomycin D, an inhibitor of transcription, if given prior to 4 h after opening, suppressed the onset of visible senescence, which occurred at about 9 h after flower opening. The isolated genes all showed upregulation. Two cell-wall related genes were upregulated early, one encoding an extensin and one a caffeoyl-CoA-3-O-methyltransferase, involved in lignin production. A pectinacetylesterase was upregulated after flower opening and might be involved in cell-wall degradation. Some identified genes showed high homology with published SAGs possibly involved in remobilisation processes: an alcohol dehydrogenase and three cysteine proteases. One transcript encoded a leucine-rich repeat receptor protein kinase, putatively involved in signal transduction. Another transcript encoded a 14-3-3 protein, also a protein kinase. Two genes have apparently not been associated previously with senescence: the first encoded a putative SEC14, which is required for Golgi vesicle transport, the second was a putative ataxin-2, which has been related to RNA metabolism. Induction of the latter has been shown to result in cell death in yeast, due to defects in actin filament formation. The possible roles of these genes in programmed cell death are discussed.
    Nuclear fragmentation and DNA degradation during programmed cell death in petals of morning glory (Ipomoea nil)
    Yamada, T. ; Takatsu, Y. ; Kasumi, K. ; Ichimura, K. ; Doorn, W.G. van - \ 2006
    Planta 224 (2006)6. - ISSN 0032-0935 - p. 1279 - 1290.
    arabidopsis-thaliana - flower tissue - ethylene - apoptosis - senescence - expression - lethality - tricolor - color - iris
    We studied DNA degradation and nuclear fragmentation during programmed cell death (PCD) in petals of Ipomoea nil (L.) Roth flowers. The DNA degradation, as observed on agarose gels, showed a large increase. Using DAPI, which stains DNA, and flow cytometry for DAPI fluorescence, we found that the number of DNA masses per petal at least doubled. This indicated chromatin fragmentation, either inside or outside the nucleus. Staining with the cationic lipophilic fluoroprobe DiOC6 indicated that each DNA mass had an external membrane. Fluorescence microscopy of the nuclei and DNA masses revealed an initial decrease in diameter together with chromatin condensation. The diameters of these condensed nuclei were about 70% of original. Two populations of nuclear diameter, one with an average diameter about half of the other, were observed at initial stages of nuclear fragmentation. The diameter of the DNA masses then gradually decreased further. The smallest observed DNA masses had a diameter less than 10% of that of the original nucleus. Cycloheximide treatment arrested the cytometrically determined changes in DNA fluorescence, indicating protein synthesis requirement. Ethylene inhibitors (AVG and 1-MCP) had no effect on the cytometrically determined DNA changes, suggesting that these processes are not controlled by endogenous ethylene.
    DNA degradation and nuclear degeneration during programmed cell death in petals of Antirrhinum, Argyranthemum, and Petunia
    Yamada, T. ; Ichimura, K. ; Doorn, W.G. van - \ 2006
    Journal of Experimental Botany 57 (2006)14. - ISSN 0022-0957 - p. 3543 - 3552.
    apoptosis - senescence - fragmentation - ethylene - expression - flowers - iris - pcd
    Programmed cell death (PCD) was studied in the petals of Antirrhinum majus, Argyranthemum frutescens, and Petunia hybrida, using DNA degradation and changes in nuclear morphology as parameters. The petals exhibit loss of turgor (wilting) as a visible symptom of PCD. DNA degradation, as shown on agarose gels, occurred in all species studied, prior to visible wilting. The number of DNA masses in all the petals of a flower, determined by flow cytometry, markedly increased in Argyranthemum and Petunia, but decreased in Antirrhinum. Many small DNA masses were observed in Argyranthemum and Petunia. The surface of each small DNA mass stained with the lipophilic fluorochrome 3,3'-dihexyloxacarbocyanine iodide (DiOC6), indicating that these masses were surrounded by a membrane. In Antirrhinum, in contrast, the chromatin fragmented into several small spherical clumps that remained inside a large membranous structure. Nuclear fragmentation, therefore, did not occur in Antirrhinum, whereas nuclear fragmentation possibly was a cause of the small DNA masses in Argyranthemum and Petunia. It is concluded that at least two contrasting nuclear morphologies exist during PCD. In the first, the chromatin fragments inside the nucleus, not accompanied¿or followed¿by nuclear fragmentation. In the second, a large number of DNA masses were observed each enveloped by a membrane. The second type was probably due, at least partially, to nuclear fragmentation
    Independent pathways leading to apoptotic cell death, oxidative burst and defence gene expression in response to elicitin in tobacco cell suspension culture
    Sasabe, M. ; Takeuchi, K. ; Kamoun, S. ; Ichinose, Y. ; Govers, F. ; Toyoda, K. ; Shiraishi, T. ; Yamada, T. - \ 2000
    European Journal of Biochemistry 267 (2000). - ISSN 0014-2956 - p. 5005 - 5013.
    We characterized pharmacologically the hypersensitive cell death of tobacco BY-2 cells that followed treatments with Escherichia coli preparations of INF1, the major secreted elicitin of the late blight pathogen Phytophthora infestans. INF1 elicitin treatments resulted in fragmentation and 180 bp laddering of tobacco DNA as early as 3 h post-treatment. INF1 elicitin also induced rapid accumulation of H2O2 typical of oxidative burst, and the expression of defense genes such as phenylalanine ammonia-lyase (PAL) gene at 1 h and 3 h after elicitin treatment, respectively. To investigate the involvement of the oxidative burst and/or the expression of defense genes in the signal transduction pathways leading to hypersensitive cell death, we analyzed the effect of several chemical inhibitors of signal transduction pathways on the various responses. The results indicated that (a) the cell death required serine proteases, Ca2 and protein kinases, (b) the oxidative burst was involved in Ca2 and protein kinase mediated pathways, but elicitin-induced AOS was neither necessary nor sufficient for cell death and PAL gene expression, and (c) the signaling pathway of PAL gene expression required protein kinases. These results suggest that the three signal transduction pathways leading to cell death, oxidative burst and expression of defense genes branch in the early stages that follow elicitin recognition by tobacco cells.
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