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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Earth System Governance : Science and Implementation Plan of the Earth System Governance Project 2018
Burch, Sarah ; Gupta, A. ; Yumie Aoki Inoue, Christina ; Kalfagianni, Agni ; Persson, Asa ; Heijden, Jeroen van der; Vervoort, Joost ; Adler, Carolina ; Bloomfield, Michael John ; Djalante, Riyanti ; Dryzek, John S. ; Galaz, Victor ; Gordon, Christopher ; Harmon, Renee ; Jinnah, Sikina ; Kim, Rakhyun E. ; Olsson, Lennart ; Leeuwen, J. van; Ramasar, Vasna ; Wapner, Paul ; Zondervan, Ruben - \ 2019
Utrecht : Earth System Governance - 128 p.
The Earth System Governance Project as a network organization: a critical assessment after ten years
Biermann, F. ; Betsill, Michele M. ; Burch, S. ; Dryzek, John ; Gordon, Christopher ; Gupta, A. ; Gupta, Joyeeta ; Inoue, Cristina ; Kalfagianni, Agni ; Kanie, Norichika ; Olsson, Lennart ; Persson, Åsa ; Schroeder, H. ; Scobie, Michelle - \ 2019
Current Opinion in Environmental Sustainability 39 (2019). - ISSN 1877-3435 - p. 17 - 23.

The social sciences have engaged since the late 1980s in international collaborative programmes to study questions of sustainability and global change. This article offers an in-depth analysis of the largest long-standing social-science network in this field: the Earth System Governance Project. Originating as a core project of the former International Human Dimensions Programme on Global Environmental Change, the Earth System Governance Project has matured into a global, self-sustaining research network, with annual conferences, numerous taskforces, research centers, regional research fellow meetings, three book series, an open access flagship journal, and a lively presence in social media. The article critically reviews the experiences of the Earth System Governance network and its integration and interactions with other programmes over the last decade.

New directions in earth system governance research
Burch, Sarah ; Gupta, A. ; Inoue, C. ; Kalfagianni, Agni ; Persson, Asa ; Gerlak, Andrea K. ; Ishii, Atsushi ; Patterson, James ; Pickering, Jonathan ; Scobie, M. ; Heijden, Jeroen van der; Vervoort, J. ; Adler, Carolina ; Bloomfield, Michael ; Djalante, Riyante ; Dryzek, John ; Galaz, Victor ; Gordon, Christopher ; Harmon, Renée ; Jinnah, Sikina ; Kim, Rakhyun E. ; Olsson, Lennart ; Leeuwen, J. van; Ramasar, Vasna ; Wapner, Paul ; Zondervan, R. - \ 2019
Earth System Governance 1 (2019). - ISSN 2589-8116 - 18 p.
Governance - Research networks - Earth system - Transformation
The Earth System Governance project is a global research alliance that explores novel, effective governance mechanisms to cope with the current transitions in the biogeochemical systems of the planet. A decade after its inception, this article offers an overview of the project's new research framework (which is built upon a review of existing earth system governance research), the goal of which is to continue to stimulate a pluralistic, vibrant and relevant research community. This framework is composed of contextual conditions (transformations, inequality, Anthropocene and diversity), which capture what is being observed empirically, and five sets of research lenses (architecture and agency, democracy and power, justice and allocation, anticipation and imagination, and adaptiveness and reflexivity). Ultimately the goal is to guide and inspire the systematic study of how societies prepare for accelerated climate change and wider earth system change, as well as policy responses.
IRE1alpha is an endogenous substrate of endoplasmic reticulum-associated degradation
Sun, Shengyi ; Shi, Guojun ; Sha, Haibo ; Ji, Yewei ; Han, Xuemei ; Shu, Xin ; Ma, Hongming ; Takamasa, Inoue ; Gao, Beixue ; Bu, Pengcheng ; Guber, Robert D. ; Shen, Xiling ; Lee, Ann H. ; Iwawaki, Takao ; Paton, Adrienne W. ; Paton, James C. ; Fang, Deyu ; Tsai, Billy ; Yates III, John R. ; Wu, Haoquan ; Kersten, Sander ; Long, Qiaoming ; Duhamel, Gerald E. ; Simpson, Kenneth W. ; Qi, Ling - \ 2015
Mus musculus - GSE70563 - PRJNA289019
Endoplasmic reticulum-associated degradation (ERAD) represents a principle quality control (QC) mechanism to clear misfolded proteins in the ER; however, its physiological significance and the nature of endogenous ERAD substrates remain largely unknown. Here we discover that IRE1alpha, the sensor of unfolded protein response (UPR), is a bona fide substrate of the Sel1L-Hrd1 ERAD complex. Mechanistically, ERAD-mediated IRE1alpha degradation occurs in a Bip-dependent manner under basal conditions and is attenuated in response to ER stress. Both intramembrane hydrophilic residues of IRE1alpha and lectin protein OS9 are required for IRE1alpha degradation. ERAD deficiency causes IRE1alpha protein stabilization, accumulation and mild activation both in vitro and in vivo, leading to cellular hypersensitivity to ER stress and inflammation. Furthermore, though enterocyte-specific Sel1L-knockout mice (Sel1LΔIEC) are viable and appear normal, they are more susceptible to experimental colitis in an IRE1alpha-dependent but CHOP-independent manner. Collectively, these results demonstrate that Sel1L-Hrd1 ERAD serves a distinct, essential function in restraint of IRE1alpha signaling in vivo by managing its protein turnover.
Within-host competition does not select for virulence in malaria parasites; studies with Plasmodium yoelii
Abkallo, H.M. ; Tangena, J.A. ; Tang, J. ; Kobayashi, N. ; Inoue, M. ; Zoungrana, A. ; Colegrave, N. ; Culleton, R. - \ 2015
PLoS Pathogens 11 (2015)2. - ISSN 1553-7366 - 20 p.
papua-new-guinea - mixed-genotype infections - rodent malaria - species infections - falciparum-malaria - genetic diversity - transmission success - anopheles-stephensi - mosquitos - children
In endemic areas with high transmission intensities, malaria infections are very often composed of multiple genetically distinct strains of malaria parasites. It has been hypothesised that this leads to intra-host competition, in which parasite strains compete for resources such as space and nutrients. This competition may have repercussions for the host, the parasite, and the vector in terms of disease severity, vector fitness, and parasite transmission potential and fitness. It has also been argued that within-host competition could lead to selection for more virulent parasites. Here we use the rodent malaria parasite Plasmodium yoelii to assess the consequences of mixed strain infections on disease severity and parasite fitness. Three isogenic strains with dramatically different growth rates (and hence virulence) were maintained in mice in single infections or in mixed strain infections with a genetically distinct strain. We compared the virulence (defined as harm to the mammalian host) of mixed strain infections with that of single infections, and assessed whether competition impacted on parasite fitness, assessed by transmission potential. We found that mixed infections were associated with a higher degree of disease severity and a prolonged infection time. In the mixed infections, the strain with the slower growth rate was often responsible for the competitive exclusion of the faster growing strain, presumably through host immune-mediated mechanisms. Importantly, and in contrast to previous work conducted with Plasmodium chabaudi, we found no correlation between parasite virulence and transmission potential to mosquitoes, suggesting that within-host competition would not drive the evolution of parasite virulence in P. yoelii.
The Tomato spotted wilt virus cell-to-cell movement protein (NSM) triggers a hypersensitive response in Sw-5 containing resistant tomato lines and Nicotiana benthamiana transformed with the functional Sw-5b resistance gene copy.
Hallwass, M. ; Silva de Oliveira, A. ; Dianese, E.C. ; Lohuis, D. ; Boiteux, L.S. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Kormelink, R.J.M. - \ 2014
Molecular Plant Pathology 15 (2014)9. - ISSN 1464-6722 - p. 871 - 880.
mosaic-virus - lycopersicon-esculentum - nonstructural protein - capsicum-chinense - coat protein - plant-cells - rna segment - tswv - tospovirus - tobacco
Although the Sw-5 gene cluster has been cloned, and Sw-5b has been identified as the functional gene copy that confers resistance to Tomato spotted wilt virus (TSWV), its avirulence (Avr) determinant has not been identified to date. Nicotiana tabacum SR1 plants transformed with a copy of the Sw-5b gene are immune without producing a clear visual response on challenge with TSWV, whereas it is shown here that N.benthamiana transformed with Sw-5b gives a rapid and conspicuous hypersensitive response (HR). Using these plants, from all structural and non-structural TSWV proteins tested, the TSWV cell-to-cell movement protein (NSM) was confirmed as the Avr determinant using a Potato virus X (PVX) replicon or a non-replicative pEAQ-HT expression vector system. HR was induced in Sw-5b-transgenic N.benthamiana as well as in resistant near-isogenic tomato lines after agroinfiltration with a functional cell-to-cell movement protein (NSM) from a resistance-inducing (RI) TSWV strain (BR-01), but not with NSM from a Sw-5 resistance-breaking (RB) strain (GRAU). This is the first biological demonstration that Sw-5-mediated resistance is triggered by the TSWV NSM cell-to-cell movement protein.
Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions
Dianese, E.C. ; Fonseca, M.E.N. ; Goldbach, R.W. ; Kormelink, R.J.M. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Boiteux, L.S. - \ 2010
Molecular Breeding 25 (2010)1. - ISSN 1380-3743 - p. 133 - 142.
spotted-wilt-virus - lycopersicon-esculentum - thrips transmission - tswv resistance - rapd markers - peruvianum - sw5
The best levels of broad-spectrum Tospovirus resistance reported in tomatoes thus far are conferred by the Sw-5 locus. This locus contains at least five paralogues (denoted Sw-5a through Sw-5e), of which Sw-5b represents the actual resistance gene. Here we evaluated a panel of seven PCR primer pairs matching different sequences within a genomic region spanning the Sw-5a and Sw-5b gene cluster. Primer efficiency evaluation was done employing tomato isolines with and without the Sw-5 locus. One primer pair produced a single and co-dominant polymorphism between susceptible and resistant isolines. Sequence analysis of these amplicons indicated that they were specific for the Sw-5 locus and their differences were due to insertions/deletions. The polymorphic SCAR amplicon encompass a conserved sequence of the promoter region of the functional Sw-5b gene, being located in the position -31 from its open reading frame. This primer pair was also evaluated in field assays and with a collection of accessions known to be either susceptible or resistant to tospoviruses. An almost complete correlation was found between resistance under greenhouse/field conditions and the presence of the marker. Therefore, this primer pair is a very useful tool in marker-assisted selection systems in a large range of tomato accessions.
Molecular mobility interpretation of water sorption isotherms of food materials by means of gravimetric NMR
Weglarz, W. ; Witek, M.M. ; Inoue, C. ; As, H. van; Duynhoven, J.P.M. van - \ 2010
In: Water properties in food, health, pharmaceutical and biological systems: ISOPOW 10 / Reid, D.S., Sajjaanantakul, T., Lillford, P.J., Charoenrein, S., Wiley-Blackwell - ISBN 9780813812731 - p. 411 - 418.
Molecular and biological characterization of Tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses
Ribeiro, S.G. ; Martin, D.P. ; Lacorte, C. ; Simoes, I.C. ; Orlandini, D.R.S. ; Inoue-Nagata, A.K. - \ 2007
Phytopathology 97 (2007)6. - ISSN 0031-949X - p. 702 - 711.
whitefly-transmitted geminiviruses - leaf-curl-virus - abutilon-mosaic-virus - dna-b - nicotiana-benthamiana - replication - emergence - sequences - disease - origin
Tomato chlorotic mottle virus (ToCMoV) is an emerging begomovirus species widely distributed throughout tomato-growing regions of Brazil. ToCMoV appears to have expanded its geographic range recently, invading tomato-growing areas that were free of begomovirus infection before 2004. We have determined the first complete genome sequence of an infectious ToCMoV genome (isolate BA-Se1), which is the first begomovirus species isolated in the northeast of Brazil. When introduced by particle bombardment into tomato, the cloned ToCMoV-[BA-Se1] DNA-A and DNA-B components caused typical chlorotic mottle symptoms. The cloned virus was whitefly-transmissible and, although it was infectious in hosts such as Nicotiana benthamiana, pepper, tobacco, and Nicandra physaloides, it was unable to infect Arabidopsis thaliana, bean, N. glutinosa, and Datura metel. Sequence and biological analyses indicate that ToCMoV-[BA-Se1] is a typical New World begomovirus sp. requiring both DNA-A and DNA-B components to establish systemic infections. Although evidence of multiple recombination events was detected within the ToCMoV-[BA-Se1] DNA-A, they apparently occurred relatively long ago, implying that recombination probably has not contributed to the recent emergence of this species.
Occurrence of begomovirus in tomato and other plant species in Central Brazil
Inoue-Nagata, A.K. ; Giordano, L.B. ; Fonseca, M.E.N. ; Ribeiro, S.G. ; Avila, L.C. ; Albuquerque, L.C. ; Boiteux, L.S. - \ 2005
The pressure head regime in the induction zone during unstable nonponding infiltration: theory and experiments
Cho, H. ; Rooij, G.H. de; Inoue, M. - \ 2005
Vadose Zone Journal 4 (2005). - ISSN 1539-1663 - p. 908 - 914.
wetting front instability - bead porous-media - fingered flow - layered soils - stability analysis - water-movement - 2 dimensions - persistence - sands - model
Fingered flow rapidly moves water and pollutants from the root zone to the groundwater through a limited fraction of the unsaturated zone, limiting the possibilities for decay and adsorption. The onset of wetting front instability and the characteristics of the flow pattern under nonponding infiltration have received limited attention. We aim to theoretically and experimentally advance our understanding of pre-fingered flow, and contrast fingered flow under ponding and nonponding conditions. We developed a Green-Ampt based expression for the pressure head in a developing induction zone (from which fingers protrude) for the time before fingers developed. A uniform, nonponding water flux was applied to the surface of two-dimensional glass bead porous media with a dry region above a capillary fringe. Microtensiometers recorded pressure heads in the induction zone. The pressure head data confirmed both the theoretical early-time pre-finger model, and a model developed earlier for late-time lateral flow toward fully developed fingers. The physically more realistic constant flux boundary condition of our experiments gave larger finger spacings and travel times, compared to the frequently used set-up with ponding infiltration into a fine-over-coarse porous medium
Potato deforming mosaic virus is possibly a variant of Tomato yellow vein streak virus
Ribeiro, S.G. ; Inoue-Nagata, A.K. ; Daniels, J. ; Avila, A.C. de - \ 2004
Fingered flow under non-ponding infiltration: development of the induction zone and the initiation of finfering
Cho, H. ; Rooij, G.H. de; Inoue, M. - \ 2004
In: Book of abstracts of the Frontis Workshop on Unsaturated Zone Modeling: Progress, Challenges and Applications, Wageningen 3-5 October 2004 / Witte, J.P.M., Kroes, J., Wageningen : Frontis - p. 103 - 103.
Pepper yellow mosaic virus, a new potyvirus in sweet-pepper. Archives of Virology
Inoue-Nagata, A.K. ; Fonseca, M.E.N. ; Resende, R.O. de; Boiteux, L.S. ; Monte, D.C. ; Dusi, A.N. ; Ávila, A.C. de; Vlugt, R.A.A. van der - \ 2002
Archives of Virology 147 (2002)4. - ISSN 0304-8608 - p. 849 - 855.
A potyvirus was found causing yellow mosaic and veinal banding in sweetpepper in Central and Southeast Brazil. The sequence analysis of the 3' terminal region of the viral RNA revealed a coat protein of 278 amino acids, followed by 275 nucleotides in the 3'-untranslated region preceding a polyadenylated tail. The virus shared 77.4% coat protein amino acid identity with Pepper severe mosaic virus, the closest Potyvirus species. The 3'-untranslated region was highly divergent from other potyviruses. Based on these results, the virus found in sweetpepper plants could be considered as a new potyvirus. The name Pepper yellow mosaic virus (PepYMV) is suggested
Factors determining vector competence and specificity for transmission of Tomato spotted wilt virus
Nagata, T. ; Inoue-Nagata, A.K. ; Lent, J. van; Goldbach, R. ; Peters, D. - \ 2002
Journal of General Virology 83 (2002). - ISSN 0022-1317 - p. 663 - 671.
Tomato chlorotic mottle virus: a novel tomato begomovirus from Brazil
Ribeiro, S.G. ; Lacorte, C. ; Inoue-Nagate, A.K. ; Carmo, I. de; Orlandini, D. ; Andrade, E.C. de; Nagata, T. ; Zerbini, F.M. - \ 2001
In: Comparative Virology : Proceedings of ssDNA Viruses of Plants, Birds, Pigs and Primates, Saint-Malo, France, 2001 Saint-Malo : S.1. - p. 47 - 47.
The pressure head regime during fingered flow in a porous medium with a capillary fringe
Rooij, G.H. de; Cho, H. ; Inoue, M. ; Toride, N. - \ 2001
In: 26th General Assembly : European Geophysical Society. - [S.l.] : 2001. (Volume 3). - ISSN 1029-7006
Finger Formation and its Relation to Lateral Flow in the Induction Zone
Rooij, G.H. de; Cho, H. ; Inoue, M. ; Toride, N. - \ 2001
In: Preferential Flow; Water Movement and Chemical Transport in the Environment : 2nd International Symposium, Honolulu, 2001 Michigan : American Society of Agricultural Engineers - ISBN 9781892769145 - p. 173 - 176.
Impeded thrips transmission of defective tomato spotted wilt virus isolates
Nagata, T. ; Inoue-Nagata, A.K. ; Prins, M. ; Goldbach, R. ; Peters, D. - \ 2000
Phytopathology 90 (2000)5. - ISSN 0031-949X - p. 454 - 459.
Two defective RNA-containing isolates (Pe-1 and 16-2) and an envelope-deficient (env(^–)) isolate of Tomato spotted wilt virus (TSWV) were tested for their transmissibility by Frankliniella occidentalis. The Pe-1 isolate contained a truncated L RNA segment that barely interfered with symptom expression and replication of the wild-type (wt) L RNA segment. This isolate was transmitted with an efficiency of 51°a value comparable to that found for wt TSWV (54Ž Isolate 16-2, which contained a genuine defective interfering L RNA as concluded from its ability to suppress wt L RNA synthesis and attenuation of symptom expression, was not transmitted at all. The midguts of all larvae that ingested Pe-1 became infected, whereas limited midgut infections were found in 24␘f the larvae that ingested 16-2. This difference in infection could be explained by the presence of a low number of infectious units in the inoculum ingested from plants as demonstrated in infection experiments and verified by northern blot analysis. The env(^–) isolate failed to infect the midgut after ingestion and could not be transmitted by any thrips stage. This isolate also cannot infect primary thrips cell cultures. Taken together, these results suggest that the envelope of TSWV contains the determinants required for binding and subsequent infection of thrips cells.
Infection and transmission of tomato spotted wilt virus mutants by thrips, Frankliniella occidentalis
Nagata, T. ; Inoue-Nagata, A.K. ; Goldbach, R. ; Peters, D. - \ 1999
Fitopatologia Brasileira 24 (1999). - ISSN 0100-4158 - p. 260 - 260.
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