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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The Sociology of Consumption in India: Towards a New Agenda
Wessel, M.G.J. van - \ 2018
In: Critical Themes in Indian Sociology / Srivastava, S., Arif, Y., Abraham, J., Delhi : Sage - ISBN 9789352807956 - p. 390 - 401.
Construction and Rescue of a Functional Synthetic Baculovirus
Shang, Yu ; Wang, Manli ; Xiao, Gengfu ; Wang, Xi ; Hou, Dianhai ; Pan, Kai ; Liu, Shurui ; Li, Jiang ; Wang, Jun ; Arif, Basil M. ; Vlak, Just M. ; Chen, Xinwen ; Wang, Hualin ; Deng, Fei ; Hu, Zhihong - \ 2017
ACS synthetic biology 6 (2017)7. - ISSN 2161-5063 - p. 1393 - 1402.
AcMNPV - baculovirus - large DNA virus - synthetic genome
Synthetic viruses provide a powerful platform to delve deeper into the nature and function of viruses as well as to engineer viruses with novel properties. So far, most synthetic viruses have been RNA viruses (<30 kb) and small DNA viruses, such as bacteriophage phiX174. Baculoviruses contain a large circular dsDNA genome of 80-180 kb and have been used as biocontrol agents and protein expression vectors. Here, we report on the first synthesis of a baculovirus based on the type species Autographa californica nucleopolyhedrovirus, AcMNPV, by a combination of PCR and transformation-associated recombination in yeast. The synthetic genome, designated AcMNPV-WIV-Syn1, is 145 299 bp comprising the complete genome of AcMNPV except for the hr4a locus that was replaced with an ∼11.5 kb cassette of bacterial and yeast artificial chromosomal elements and an egfp gene. Sf9 insect cells were transfected with AcMNPV-WIV-Syn1 DNA and progeny virus was examined by electron microscopy, and assayed in one-step growth curves and oral infectivity. The results conclusively showed that the rescued virus AcMNPV-WIV-Syn1 had structural and biological properties comparable to the parental virus. We validated a proof of concept that a bona fide baculovirus can be synthesized. The new platform allows manipulation at any or multiple loci and will facilitate future studies such as identifying the minimal baculovirus genome and construction of better expression vectors. This is the largest DNA virus synthesized so far, and its success is likely to be the impetus to stimulate the fields of other large DNA viruses such as herpesviruses and poxviruses.
GHG mitigation of agricultural peatlands requires coherent policies
Regina, Kristiina ; Budiman, Arif ; Greve, Mogens H. ; Grønlund, Arne ; Kasimir, Åsa ; Lehtonen, Heikki ; Petersen, S.O. ; Smith, Pete ; Wosten, Henk - \ 2016
Climate Policy (2016). - ISSN 1469-3062 - p. 522 - 541.
agriculture - GHG - land use - mitigation - peat - policies

As soon as peat soil is drained for agricultural production, the peat starts to degrade, which causes emissions to the atmosphere. In countries with large peatland areas, the GHG mitigation potential related to management of these soils is often estimated as the highest amongst the measures available in agriculture. Although the facts are well known, the policies leading to diminished emissions are often difficult to implement. We have analysed the reasons why the mitigation potential is not fully utilized and what could be done better in national implementation of climate policies. Four cases are used to illustrate the necessary steps to reach mitigation targets: determining the amount and properties of peat soils, estimating the potential, costs and feasibility of the mitigation measures, and selecting and implementing the best measures. A common feature for all of the cases was that national and international climate policies have increased the public interest in GHG emissions from peat soils and increased the pressure for mitigation. Basically the same factors restrict the implementation of mitigation measures in all countries with significant peat soil areas. The most important of these is lack of policy coherence, e.g. ignoring climate policies when planning land use or agricultural policies. We conclude that GHG mitigation is achieved only if other policies, especially national regulations and strategies, are in line with climate policies.

Policy relevance

Agricultural peat soils could be used to help reach GHG mitigation goals in many countries, but the full potential of mitigation of peat soils is not used. Although peatland cultivation inevitably leads to loss of the whole peat layer and high emissions, there are few incentives or regulation to effectively minimize these losses. This article discusses the possibilities to reduce GHG emissions from agricultural peat soils, with specific emphasis on the barriers of implementing mitigation measures nationally. The lessons learned from the selected cases emphasize the role of all policy makers and their cooperation in planning coherent policies for achieving the goals determined by climate policies.

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factorsin flower development
Pajoro, A. ; Madrigal, P. ; Muiño, J.M. ; Tomas Matus, J. ; Jin, J. ; Mecchia, M.A. ; Debernardi, J.M. ; Palatnik, J.F. ; Balazadeh, S. ; Arif, M. ; Ó’Maoiléidigh, D.S. ; Wellmer, F. ; Krajewski, P. ; Riechmann, J.L. ; Angenent, G.C. - \ 2014
Genome Biology 15 (2014)3. - ISSN 1474-7596
floral organ identity - arabidopsis-thaliana - chip-seq - genomic regions - molecular-basis - target genes - zinc-finger - expression - protein - dna
Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
Quantitative and specific detection of the biocontrol agent, Serratia plymuthica, in plant extracts using a real-time TaqMan® assay
Czajkowski, R.L. ; Wolf, J.M. van der - \ 2012
Journal of Applied Genetics 53 (2012)4. - ISSN 1234-1983 - p. 457 - 467.
biological-control agents - marcescens cells - genus serratia - grass grub - bacteria - identification - strains - soil - rhizosphere - antifungal
A Serratia plymuthica-specific TaqMan® assay was designed based on the consensus nucleotide sequence from the 3'- end of the luxS gene present in all S. plymuthica strains tested. The specificity of the assay was demonstrated by testing 21 Serratia spp. strains and 30 isolates belonging to various species that can potentially coexist with S. plymuthica in the same environment. Positive reactions in the TaqMan® assay were observed only for S. plymuthica isolates and not for other bacteria. The TaqMan® assay could detect down to 1.95 ng of S. plymuthica DNA, down to 5 bacterial cells per reaction (100 cfu ml-1) in vitro, down to 50 bacterial cells per reaction (1,000 cfu ml-1) in spiked potato root extracts and down to 5 bacterial cells per reaction (100 cfu ml-1) in spiked potato haulm extracts. We used this assay to quantify S. plymuthica A30 cells in potato and tomato haulms and roots grown from S. plymuthica A30-inoculated potato seed tubers and tomato seeds. The results were comparable with the spread-plating of plant extracts on a newly developed S. plymuthica A30 selective medium (CVTR2Arif). The TaqMan® assay can be used to quantify S. plymuthica isolates in different ecosystems and in complex substrates
Baculoviridae
Herniou, E.A. ; Arif, B.M. ; Becnel, J.J. ; Blissard, G.W. ; Bonning, B.C. ; Harrison, R. ; Jehle, J.A. ; Theilmann, D.A. ; Vlak, J.M. - \ 2011
In: Virus Taxonomy, IXth Report of the International Committee on Taxonomy of Viruses / Adams, M.J., King, A.M.Q., Cartsens, E.B., Lefkowitz, E.J., Oxford : Elsevier - ISBN 9780123846846 - p. 163 - 174.
An active DNA photolyase (AMV025) from Amsacta moorei entomopoxvirus
Nalcacioglu, R. ; Sezen, K. ; Ince, I.A. ; Demirbag, Z. ; Vlak, J.M. ; Arif, B.M. ; Oers, M.M. van - \ 2009
In: Abstract Book of the 42nd Annual Meeting of the Society for Invertebrate Pathology, Park City, Utah, USA, 16 - 20 August, 2009. - Park City, Utah : - p. 91 - 91.
Identification of pif-2, a third conserved baculovirus gene required for per os infection of insect
Pijlman, G.P. ; Pruijssers, A. ; Vlak, J.M. - \ 2003
Journal of General Virology 84 (2003). - ISSN 0022-1317 - p. 2041 - 2049.
nuclear polyhedrosis-virus - spodoptera-exigua - genome sequence - deletion mutants - escherichia-coli - protein-kinase - cell-line - nucleopolyhedrovirus - virulence - dna
Infection of cultured insect cells with Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) resulted in the generation of mutants with major genomic deletions. Some of the mutants lacked the ability to infect S. exigua larvae per os. The gene(s) responsible for this phenotype in SeMNPV was mapped within a contiguous sequence encoding ORFs 29-35. In this paper we have shown that SeMNPV ORFs 15-35 (including genes encoding cathepsin, chitinase, GP37, PTPT-2, EGT, PKIP-1 and ARIF-1) are not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection. By site-specific deletion mutagenesis of a full-length infectious clone of SeMNPV (bacmid) using ET recombination in E. coli, a series of SeMNPV bacmid mutants with increasing deletions in ORFs 15-35 was generated. Analyses of these mutants indicated that a deletion of SeMNPV ORF35 (Se35) resulted in loss of oral infectivity of polyhedral occlusion bodies. Reinsertion of ORF35 in SeMNPV bacmids lacking Se35 rescued oral infectivity. We propose the name pif-2 for Se35 and its baculovirus homologues (e.g. Autographa californica MNPV ORF22), by analogy to a different gene recently characterized in Spodoptera littoralis NPV, which was designated per os infectivity factor (pi. Similar to the p74 gene, which encodes an essential structural protein of the occlusion-derived virus envelope, pif and pif-2 belong to a group of 30 genes that are conserved among the Baculoviridae.
Nucleotide sequence and transcriptional analysis of a putative basic DNA-binding protein of Helicoverpa armigera nuclepolyhedrovirus
Wang, H. ; Chen, X. ; Arif, B.M. ; Vlak, J.M. ; Hu, Z. - \ 2001
Virus Genes 22 (2001). - ISSN 0920-8569 - p. 113 - 120.
A putative basic DNA-binding protein (BDBP) gene was identified in the fragment EcoRI-K of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV) genome. The ORF is 330 nucleotides long encoding a basic protein of 109 amino acids with a molecular mass of 11.6 kDa. It is the first BDBP identified in single nucleocapsid NPVs and a homologue of Autographa californica MNPV (AcMNPV) P6.9. A consensus late transcription motif, ATAAG, was found at 57 nt upstream of the translational start codon and a polyadenylation signal was observed at 172 nt downstream of the stop codon. A major transcript of 620 nt was first observed in HearNPV-infected Hz2e5 cells 16 h post infection. Primer extension analysis revealed that this transcript initiated from the first residue of the consensus ATAAG late transcription start motif. Comparison with other baculoviral BDBPs showed that they all contained two conserved cAMP- and cGMP-dependent protein kinase phosphorylation motifs, R-R-R-S. The HearNPV P6.9 homologue is the longest BDBP found so far in baculoviruses.
Sequence analysis of the putative v-cathepsin gene of Heliothis armigera single-nucleocapsid baculovirus
Liu, L. ; Chen, X. ; Sun, X. ; Lauzon, H. ; Vlak, J.M. ; Arif, B.M. ; Hu, Z. - \ 2001
Virologica Sinica 16 (2001)3. - ISSN 1003-5125 - p. 229 - 235.
Genomic organization of Helicoverpa armigera single-nucleocapsid nucleopoly-hedrovirus
Chen, X. ; Li, M. ; Sun, X. ; Arif, B.M. ; Hu, Z.H. ; Vlak, J.M. - \ 2000
Archives of Virology 145 (2000). - ISSN 0304-8608 - p. 2539 - 2555.
Nucleotide sequence and transcription analysis of a basic DNA-binding protein of Helicoverpa armigera SNPV
Wang, H. ; Chen, X. ; Li, M. ; Peng, H. ; Sun, X. ; Arif, B.M. ; Vlak, J.M. ; Hu, Z.H. - \ 1999
In: 32nd Annual Meeting of the Society for Invertebrate Pathology (SIP) : 23 - 27 August 1999, Irvine, California, USA : book of abstracts / [by the] University of California. - [S.l.] : [s.n.], 1999 - p. 79 - 79.
Genetic organization of the BamHI-H region of the single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria (BusuNPV)
Luo, B. ; Chen, X. ; Sun, X. ; Wang, H. ; Peng, H. ; Hu, Z. ; Arif, B.M. ; Vlak, J.M. - \ 1999
Virologica Sinica 14 (1999)4. - ISSN 1003-5125 - p. 333 - 342.
Genome parity studies of Choristoneura fumiferana MNPV and sequenced genomes of other nucleopolyhedroviruses
Dominy, C.N. ; Vlak, J.M. ; Arif, B.M. ; Krell, P.J. - \ 1999
In: 32nd Annual Meeting of the Society for Invertebrate Pathology (SIP) : 23 - 27 August 1999, Irvine, California, USA : book of abstracts / [by the] University of California. - [S.l.] : [s.n.], 1999 - p. 32 - 33.
Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome.
Hu, Z.H. ; Arif, B.M. ; Jin, F. ; Martens, J.W.M. ; Chen, X.W. ; Sun, J.S. ; Zuidema, D. ; Goldbach, R.W. ; Vlak, J.M. - \ 1998
Journal of General Virology 79 (1998). - ISSN 0022-1317 - p. 2841 - 2851.
In vivo cloning of Helicoverpa armigera single nucleocapsid nuclear polyhedrosis virus genotypes.
Sun, X. ; Zhang, G. ; Zhang, Z. ; Hu, Z.H. ; Vlak, J.M. ; Arif, B.M. - \ 1998
Virologica Sinica 13 (1998). - ISSN 1003-5125 - p. 83 - 88.
Genetic organization of the HindIII-I region of the single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria.
Hu, Z.H. ; Arif, B.M. ; Sun, J.S. ; Chen, X.W. ; Zuidema, D. ; Goldbach, R.W. ; Vlak, J.M. - \ 1998
Virus Research 55 (1998). - ISSN 0168-1702 - p. 71 - 82.
The single-nucleocapsid nucleopolyhedrovirus of Buzura suppressaria encodes a p10 protein.
Oers, M.M. van; Hu, Z.H. ; Arif, B.M. ; Strien, E.A. van; Lent, J.W.M. van; Vlak, J.M. - \ 1998
Journal of General Virology 79 (1998). - ISSN 0022-1317 - p. 1553 - 1562.
Distinct gene distribution of the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome: developments of the molecular evolution of baculoviruses.
Hu, Z.H. ; Arif, B.M. ; Jin, F. ; Martens, W.M. ; Chen, X.W. ; Sun, J.S. ; Zuidema, D. ; Goldbach, R.W. ; Vlak, J.M. - \ 1998
In: 3rd International Youth Biologist's Meeting, Xian, People's Republic of China - p. 74 - 74.
Genomics of Heliothis armigera single-nucleocapsid baculovirus.
Chen, X. ; Li, M. ; Sun, X. ; Arif, B.M. ; Hu, Z. ; Vlak, J.M. - \ 1998
In: 7th International Colloquium on Invertebrate Pathology and Microbial Control, Sapporo, Japan - p. 21 - 22.
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