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 C-Termini of the baculovirus per os infectivity factors 1 and 2 mediate ODV oral infectivity by facilitating the binding of PIF0 and PIF8 to the core of the entry complex
    Boogaard, Bob ; Ortega Murillo, Fabiola D. ; Sminia, Alexander L. ; Theilmann, David A. ; Lent, Jan W.M. Van; Oers, Monique M. Van - \ 2020
    Journal of General Virology 101 (2020)5. - ISSN 0022-1317 - p. 553 - 564.
    AcMNPV. - Baculovirus - Oral Infectivity - PIF - PIF complex

    Oral infection of caterpillars by baculoviruses is initiated by occlusion-derived virus particles (ODVs) that infect midgut epithelium cells. The ODV envelope therefore contains at least ten different proteins, which are called per os infectivity factors (PIFs). Nine of these PIFs form the so-called ODV entry complex that consists of a stable core formed by PIF1, 2, 3 and 4, to which the other PIFs [PIF0, 6, 7, 8 and 9 (ac108)] bind with lower affinity. PIF1 and 2 are not only essential for complex formation, but also mediate ODV-binding to the epithelial brush border, probably via the C-Termini. To study the involvement of these PIFs during midgut infection in greater detail, we assessed the oral infectivity and the ability to form the complex of a series of PIF1 and PIF2 C-Terminal truncation mutants of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), which were constructed in this study. Limited truncation of either PIF1 or 2 already severely impaired the ODV oral infectivity, but did not affect the formation of the core complex. However, the entry complex as a whole was not assembled in these mutants as PIF0 and 8 failed to bind to the core. This suggests that the interactions between the core and the loosely associated PIFs are important for the ODV infectivity and that complex formation complicates the determination of the exact roles of PIF1 and 2 during midgut infection. We also showed that the presence of PIF0, 6 and the ZF-domain of PIF8 are crucial for complex formation.

    Dietary patterns are related to cognitive functioning in elderly enriched with individuals at increased risk for Alzheimer’s disease
    Wesselman, L.M.P. ; Lent, Melo van; Schröder, A. ; Rest, O. van de; Peters, O. ; Menne, F. ; Fuentes, M. ; Priller, J. ; Spruth, E.J. ; Altenstein, S. ; Schneider, A. ; Fließbach, K. ; Roeske, S. ; Wolfsgruber, S. ; Kleineidam, L. ; Spottke, A. ; Pross, V. ; Wiltfang, J. ; Vukovich, R. ; Schild, A.K. ; Düzel, E. ; Metzger, C.D. ; Glanz, W. ; Buerger, K. ; Janowitz, D. ; Perneczky, R. ; Tatò, M. ; Teipel, S. ; Kilimann, I. ; Laske, C. ; Buchmann, M. ; Ramirez, A. ; Sikkes, S.A.M. ; Jessen, F. ; Flier, W.M. van der; Wagner, M. - \ 2020
    European Journal of Nutrition (2020). - ISSN 1436-6207
    Cognition - Dementia - Dietary patterns - Mediterranean diet - MIND diet

    Purpose: To investigate cross-sectional associations between dietary patterns and cognitive functioning in elderly free of dementia. Methods: Data of 389 participants from the German DELCODE study (52% female, 69 ± 6 years, mean Mini Mental State Score 29 ± 1) were included. The sample was enriched with elderly at increased risk for Alzheimer’s disease (AD) by including participants with subjective cognitive decline, mild cognitive impairment (MCI) and siblings of AD patients. Mediterranean and MIND diets were derived from 148 Food Frequency Questionnaire items, and data-driven patterns by principal component analysis (PCA) of 39 food groups. Associations between dietary patterns and five cognitive domain scores were analyzed with linear regression analyses adjusted for demographics (model 1), and additionally for energy intake, BMI, other lifestyle variables and APOe4-status (model 2). For PCA-derived dietary components, final model 3 included all other dietary components. Results: In fully adjusted models, adherence to Mediterranean and MIND diet was associated with better memory. The ‘alcoholic beverages’ PCA component was positively associated with most cognitive domains. Exclusion of MCI subjects (n = 60) revealed that Mediterranean and MIND diet were also related to language functions; associations with the alcoholic beverages component were attenuated, but most remained significant. Conclusion: In line with data from elderly population samples, Mediterranean and MIND diet and some data-derived dietary patterns were related to memory and language function. Longitudinal data are needed to draw conclusions on the putative effect of nutrition on the rate of cognitive decline, and on the potential of dietary interventions in groups at increased risk for AD.

    Climate adaptation, urban regeneration and brownfield reclamation : a literature review on landscape quality in large-scale transformation projects
    Oudes, Dirk ; Stremke, Sven - \ 2020
    Landscape Research (2020). - ISSN 0142-6397
    energy landscape - energy transition - Environmental design - landscape architecture

    The transition to renewable energy is a powerful driver for large-scale landscape transformation. Environmental design is increasingly engaged in this transition, but little is known about purposefully designed renewable energy landscapes. To improve the design of large-scale energy landscapes we reviewed the literature on three innovative large-scale landscape transformations: Room for the River Nijmegen-Lent (The Netherlands), Queen Elizabeth Olympic Park (UK) and Freshkills Park (USA). We analysed 61 papers on landscape quality and the role of design, governments and participation. Concerning landscape quality, literature reports on functionality and certain aspects of experience rather than firmness (future values) of the transformation. While designers played an important role in large-scale landscape transformations, local governments seem not to be in control of the decision-making and participation was limited. The three cases illustrate how executed projects influence the discourse on landscape transformation and provide valuable insights for the design of renewable energy landscapes.

    Baculovirus per os infectivity : a complex matter
    Boogaard, Bob - \ 2020
    Wageningen University. Promotor(en): M.M. van Oers, co-promotor(en): J.W.M. van Lent. - Wageningen : Wageningen University - ISBN 9789463952132 - 159

    Insect larvae are infected by baculoviruses when they consume plant material that is contaminated with occlusion bodies (OBs). OBs are polyhedral shaped particles of crystallized protein (polyhedrin or granulin), in which the occlusion derived viruses (ODVs) are embedded. Upon ingestion of the OBs, the ODVs are released in the alkaline lumen of the midgut and infect the midgut epithelial cells. To be infectious for these cells under alkaline conditions, the ODV envelope contains a set of proteins, which are called per os infectivity factors or PIFs. Eight different PIFs had been identified at the start of this research, of which six were known to participate in the formation of a large complex: the ODV entry complex. Presently, ten different PIFs are known, of which nine form the entry complex. This complex has a stable core that is formed by PIF1 to 4, which even resists treatment with denaturing and reducing agents (SDS and β-mercaptoethanol), and five additional PIFs (PIF0 and PIF6 to 9), which are associated to the complex more loosely. All these individual components are essential for complex formation. PIF5 is the only PIF-protein that is not a constituent of the entry complex.  

    Our initial studies with pif deletion mutant viruses were hampered by the disappearance of not only the targeted, but also non-targeted PIFs, when the OBs were produced in insect larvae, while the various PIFs were all detectable for  the wild type virus. However, those remaining PIFs were found again in these mutant viruses when the larval derived OBs were treated with heat prior to ODV isolation, or when the OBs were produced in cultured insect cells. These observations showed that proteases from the host, which had been reported to be co-occluded in the OBs, are able to degrade PIF proteins when complex formation is disrupted, as was the case in the various pif deletion mutant viruses. These observations provided a first clue on why the PIFs form a complex, which might be important to resist proteolytic degradation by proteases in the gut of the host.

    Previous research in our laboratory had identified viral protein AC108 as a PIF1 interaction partner in a co-immunoprecipitation study, indicating that this protein might be involved in oral infectivity as well. The research presented in this thesis demonstrated that mutation of the ac108 gene from the viral genome completely abolished the oral infectivity of ODVs, which was recovered when this gene was repaired. Further protein analyses revealed that AC108 is a loosely associated but nevertheless an essential component of the ODV entry complex. This protein was therefore designated as PIF9.

    The biological function of PIF9 was further investigated by the generation of fluorescently labelled ODVs of the pif9 mutant. These virus particles were then combined with isolated midgut cells of Spodoptera exigua larvae and monitored by confocal microscopy in a time lapse experiment. It was observed that in absence of PIF9, the ODVs still bind to the midgut cell brush border, but that the nucleocapsids failed to enter the cell, in contrast to fluorescent ODVs that have all PIFs. Fluorescent ODVs were also generated for a pif3 deletion mutant as it had been shown previously by others that this (complex deficient) mutant is able to bind and fuse with the host cell plasma membrane as the wild type virus, but nevertheless fails to establish a midgut infection. Our analysis with the confocal microscope showed that this mutant displays the same phenotype as the pif9 deletion mutant virus: ODV binding, but no entry of the nucleocapsids. We therefore proposed a two-step fusion process, in which first the outer leaflets of the lipid bilayers fuse and subsequently the inner leaflets. PIF3 might be important to complete the fusion process by aiding fusion of the inner leaflets of the lipid bilayers.  

    PIF1 and 2 had been reported to be important for ODV binding and were later also shown to be crucial for the formation of the ODV entry complex. Furthermore, ODV binding had been shown to be one of the viral host range determinants and as most baculoviruses have a narrow host range, we hypothesized that the more variable C-terminal parts of PIF1 and 2 are important for host interaction, while the highly conserved N-terminal parts are needed for complex formation. However, limited C-terminal truncation of either PIF1 or 2 abolished formation of the entry complex as PIF0 and 8 failed to bind the stable core in the truncation mutants. The lost ability to form the entry complex in the truncation mutants was accompanied by a severely hampered oral infectivity in S. exigua larvae. Some larvae incidentally got infected by one of the truncation mutants despite abolished complex formation. It was therefore speculated that although the ODV entry complex is the main determinant for the infectivity of ODVs, additional factors are present in the ODV that is able to incidentally cause infections in absence of the entry complex.

    To determine the context in which the PIFs function, the interaction partners were mapped of three loosely associated components of the entry complex (PIF6, 8 and 9) and the single solitary PIF, PIF5. These analyses revealed that the PIFs interact with a plethora of viral proteins with a wide variety of functions, from nucleocapsid assembly to OB formation. PIF5 also interacted with two components of the entry complex, PIF0 and 1. This indicated that PIF0 and 1 are not only present in the ODV envelope as part of the entry complex, but also occur outside the complex where these proteins interact with PIF5. This study shows that the PIFs not only interact with each other to form the entry complex, but are part of a network of protein interactions in ODVs. The biological significance of these interactions for midgut infection remains enigmatic.

    Development of a trained immunity and resilience model for testing of orally applied β-glucans
    Moerings, Bart ; Graaff, Priscilla de; Wichers, H.J. ; Garssen, Johan ; Witkamp, R.F. ; Debets, R. ; Mes, J.J. ; Bergenhenegouwen, Jeroen van; Govers, C.C.F.M. - \ 2019
    Herpes simplex virus 1 can enter dynamin 1 and 2 double- knockout fibroblasts
    Möckel, Maureen ; Rahn, Elena ; La Cruz, Nydia De; Wirtz, Lisa ; Lent, Jan W.M. Van; Pijlman, Gorben P. ; Knebel-Mörsdorf, Dagmar - \ 2019
    Journal of Virology 93 (2019)16. - ISSN 0022-538X
    Dynamin - Dynamin DKO - Dynasore - Endocytosis - HSV-1 - Low temperature - Murine embryonic fibroblasts - Semliki Forest virus - Virus entry

    Dynamin GTPases, best known for their role in membrane fission of endocytic vesicles, provide a target for viruses to be exploited during endocytic uptake. Recently, we found that entry of herpes simplex virus 1 (HSV-1) into skin cells depends on dynamin, although our results supported that viral internalization occurs via both direct fusion with the plasma membrane and via endocytic pathways. To further explore the role of dynamin for efficient HSV-1 entry, we utilized conditional dynamin 1 and dynamin 2 double-knockout (DKO) fibroblasts as an experimental tool. Strikingly, HSV-1 entered control and DKO fibroblasts with comparable efficiencies. For comparison, we infected DKO cells with Semliki Forest virus, which is known to adopt clathrin-mediated endocytosis as its internalization pathway, and observed efficient virus entry. These results support the notion that the DKO cells provide alternative pathways for viral uptake. Treatment of cells with the dynamin inhibitor dynasore confirmed that HSV-1 entry depended on dynamin in the control fibroblasts. As expected, dynasore did not interfere with viral entry into DKO cells. Electron microscopy of HSV-1-infected cells suggests viral entry after fusion with the plasma membrane and by endocytosis in both dynaminexpressing and dynamin-deficient cells. Infection at low temperatures where endocytosis is blocked still resulted in HSV-1 entry, although at a reduced level, which suggests that nonendocytic pathways contribute to successful entry. Overall, our results strengthen the impact of dynamin for HSV-1 entry, as only cells that adapt to the lack of dynamin allow dynamin-independent entry. IMPORTANCE The human pathogen herpes simplex virus 1 (HSV-1) can adapt to a variety of cellular pathways to enter cells. In general, HSV-1 is internalized by fusion of its envelope with the plasma membrane or by endocytic pathways, which reflects the high adaptation to differences in its target cells. The challenges are to distinguish whether multiple or only one of these internalization pathways leads to successful entry and, furthermore, to identify the mode of viral uptake. In this study, we focused on dynamin, which promotes endocytic vesicle fission, and explored how the presence and absence of dynamin can influence viral entry. Our results support the idea that HSV-1 entry into mouse embryonic fibroblasts depends on dynamin; however, depletion of dynamin still allows efficient viral entry, suggesting that alternative pathways present upon dynamin depletion can accomplish viral internalization.

    Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice
    Rogier, Rebecca ; Ederveen, Thomas H.A. ; Wopereis, Harm ; Hartog, Anita ; Boekhorst, Jos ; Hijum, Sacha A.F.T. Van; Knol, Jan ; Garssen, Johan ; Walgreen, Birgitte ; Helsen, Monique M. ; Kraan, Peter M. Van Der; Lent, Peter L.E.M. Van; De Loo, Fons A.J. Van; Abdollahi-Roodsaz, Shahla ; Koenders, Marije I. - \ 2019
    PLoS ONE 14 (2019)7. - ISSN 1932-6203

    The intestinal microbiome is perturbed in patients with new-onset and chronic autoimmune inflammatory arthritis. Recent studies in mouse models suggest that development and progression of autoimmune arthritis is highly affected by the intestinal microbiome. This makes modulation of the intestinal microbiota an interesting novel approach to suppress inflammatory arthritis. Prebiotics, defined as non-digestible carbohydrates that selectively stimulate the growth and activity of beneficial microorganisms, provide a relatively non-invasive approach to modulate the intestinal microbiota. The aim of this study was to assess the therapeutic potential of dietary supplementation with a prebiotic mixture of 90% short-chain galacto-oligosaccharides and 10% long-chain fructo-oligosaccharides (scGOS/lcFOS) in experimental arthritis in mice. We here show that dietary supplementation with scGOS/ lcFOS has a pronounced effect on the composition of the fecal microbiota. Interestingly, the genera Enterococcus and Clostridium were markedly decreased by scGOS/lcFOS dietary supplementation. In contrast, the family Lachnospiraceae and the genus Lactobacillus, both associated with healthy microbiota, increased in mice receiving scGOS/lcFOS diet. However, the scGOS/lcFOS induced alterations of the intestinal microbiota did not induce significant effects on the intestinal and systemic T helper cell subsets and were not sufficient to reproducibly suppress arthritis in mice. As expected, we did observe a significant increase in the bone mineral density in mice upon dietary supplementation with scGOS/lcFOS for 8 weeks. Altogether, this study suggests that dietary scGOS/lcFOS supplementation is able to promote presumably healthy gut microbiota and improve bone mineral density, but not inflammation, in arthritis-prone mice.

    Characterization of Soybean yellow shoot virus, a New Member of the Family Potyviridae Infecting Soybean Plants in Brazil
    Figueira, Antonia Dos Reis ; Geraldino-Duarte, Priscilla S. ; Pinzón Nuñez, Andrés Mauricio ; Lent, Jan van; Galvino-Costa, Suellen B.F. ; Farman, M. ; Goodin, Michael M. - \ 2019
    Plant Disease 103 (2019)6. - ISSN 0191-2917 - p. 1172 - 1180.

    A new virus species, belonging to the family Potyviridae and capable of infecting most of the soybean cultivars grown in Brazil, was collected in Lavras, Minas Gerais, Brazil, and named Soybean yellow shoot virus (SoyYSV). In this study, the complete 9,052-nucleotide genome of SoyYSV was determined and the structural, biological, and molecular properties of the virus were investigated. The SoyYSV genome encoded a single polyprotein that could be subsequently cleaved, generating 11 proteins. The SoyYSV genome shared 49% nucleotide and 36% amino acid sequence identity with Blackberry virus Y. However, the P1 protein of SoyYSV was much smaller and lacked the ALK1 domain characteristic of the genus Brambyvirus. Electron microscopy revealed flexuous filamentous virus particles, 760 to 780 nm in length, and cytoplasmic inclusions typical of those found in plant cells infected with Potyviridae species. In addition to soybean, SoyYSV infected species in the Amaranthaceae, Caricaceae, Fabaceae, and Solanaceae families. Among the most common potyviruses present in Brazil, only SoyYSV induced local necrotic lesions in Carica papaya L. SoyYSV was transmissible by Myzus persicae and Aphis gossypii but lacked the HC-Pro domain required for aphid transmission in other potyviruses. No seed transmission in soybean was observed.

    Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

    The baculovirus Ac108 protein is a per os infectivity factor and a component of the ODV entry complex
    Boogaard, Bob ; Evers, Felix ; Lent, Jan W.M. van; Oers, Monique M. van - \ 2019
    Journal of General Virology 100 (2019)4. - ISSN 0022-1317 - p. 669 - 678.
    m91 - ODV entry complex - per osinfectivity factor - PIF - PIF9 - sf58

    Wild-type ODVs (Wt) have an intact ODV entry complex in their envelope and are orally infectious towards insect larvae (left panel). In the absence of Ac108 (mut ac108), the stable core is still present but nevertheless fails to form an entry complex, affecting the ODV oral infectivity (right panel). The components of the core complex are depicted in yellow and the loosely associated components are depicted in red. PIF7 is depicted in green as its affinity with the complex is currently not known.Baculoviruses orally infect insect larvae when they consume viral occlusion bodies (OBs). OBs consist of a crystalline protein matrix in which the infectious virus particles, the occlusion-derived viruses (ODVs), are embedded. The protein matrix dissolves in the alkaline environment of the insect's midgut lumen. The liberated ODVs can then infect midgut endothelial cells through the action of at least nine different ODV-envelope proteins, called per os infectivity factors (PIFs). These PIF proteins mediate ODV oral infectivity, but are not involved in the systemic spread of the infection by budded viruses (BVs). Eight of the known PIFs form a multimeric complex, named the ODV entry complex. In this study, we show for Autographa californica multiple nucleopolyhedrovirus that mutation of the ac108ORF abolishes the ODV oral infectivity, while production and infectivity of the BVs remains unaffected. Furthermore, repair of the ac108 mutant completely recovered oral infectivity. With an HA-tagged repair mutant, we were able to demonstrate by Western analysis that the Ac108 protein is a constituent of the ODV entry complex, where the formation was abolished in the absence of this protein. Based on these results, we conclude that ac108 encodes a per os infectivity factor (PIF9) that is also an essential constituent of the ODV entry complex.

    Impacts of Mauritia flexuosa degradation on the carbon stocks of freshwater peatlands in the Pastaza-Marañón river basin of the Peruvian Amazon
    Bhomia, Rupesh Kumar ; Lent, Jeffrey van; Grandez Rios, Julio M. ; Hergoualc’h, Kristell ; Honorio Coronado, Eurídice N. ; Murdiyarso, Daniel - \ 2019
    Mitigation and Adaptation Strategies for Global Change 24 (2019)4. - ISSN 1381-2386 - p. 645 - 668.
    Amazon basin - Forest degradation - Peat swamp forest - River dynamics - Soil carbon

    Tropical peat swamp forests (PSF) are characterized by high quantities of carbon (C) stored as organic soil deposits due to waterlogged conditions which slows down decomposition. Globally, Peru has one of the largest expanse of tropical peatlands, located primarily within the Pastaza-Marañón river basin in the Northwestern Peru. Peatland forests in Peru are dominated by a palm species—Mauritia flexuosa, and M. flexuosa-dominated forests cover ~ 80% of total peatland area and store ~ 2.3 Pg C. However, hydrologic alterations, land cover change, and anthropogenic disturbances could lead to PSF’s degradation and loss of valuable ecosystem services. Therefore, evaluation of degradation impacts on PSF’s structure, biomass, and overall C stocks could provide an estimate of potential C losses into the atmosphere as greenhouse gases (GHG) emissions. This study was carried out in three regions within Pastaza-Marañón river basin to quantify PSF’s floristic composition and degradation status and total ecosystem C stocks. There was a tremendous range in C stocks (Mg C ha −1 ) in various ecosystem pools—vegetation (45.6–122.5), down woody debris (2.1–23.1), litter (2.3–7.8), and soil (top 1 m; 109–594). Mean ecosystem C stocks accounting for the top 1 m soil were 400, 570, and 330 Mg C ha −1 in Itaya, Tigre, and Samiria river basins, respectively. Considering the entire soil depth, mean ecosystem C stocks were 670, 1160, and 330 Mg C ha −1 in Itaya, Tigre, and Samiria river basins, respectively. Floristic composition and calcium to Magnesium (Ca/Mg) ratio of soil profile offered evidence of a site undergoing vegetational succession and transitioning from minerotrophic to ombrotrophic system. Degradation ranged from low to high levels of disturbance with no significant difference between regions. Increased degradation tended to decrease vegetation and forest floor C stocks and was significantly correlated to reduced M. flexuosa biomass C stocks. Long-term studies are needed to understand the linkages between M. flexuosa harvest and palm swamp forest C stocks; however, river dynamics are important natural drivers influencing forest succession and transition in this landscape.

    Greenhouse gas emissions along a peat swamp forest degradation gradient in the Peruvian Amazon : soil moisture and palm roots effects
    Lent, Jeffrey van; Hergoualc’h, Kristell ; Verchot, Louis ; Oenema, Oene ; Groenigen, Jan Willem van - \ 2019
    Mitigation and Adaptation Strategies for Global Change 24 (2019)4. - ISSN 1381-2386 - p. 625 - 643.
    CH - CO - GHG - Mauritia flexuosa - NO - Peat swamp forest - Pneumatophores - Tropical peatland - Water-filled pore space
    Tropical peatlands in the Peruvian Amazon exhibit high densities of Mauritia flexuosa palms, which are often cut instead of being climbed for collecting their fruits. This is an important type of forest degradation in the region that could lead to changes in the structure and composition of the forest, quality and quantity of inputs to the peat, soil properties, and greenhouse gas (GHG) fluxes. We studied peat and litterfall characteristics along a forest degradation gradient that included an intact site, a moderately degraded site, and a heavily degraded site. To understand underlying factors driving GHG emissions, we examined the response of in vitro soil microbial GHG emissions to soil moisture variation, and we tested the potential of pneumatophores to conduct GHGs in situ. The soil phosphorus and carbon content and carbon-to-nitrogen ratio as well as the litterfall nitrogen content and carbon-to-nitrogen ratio were significantly affected by forest degradation. Soils from the degraded sites consistently produced more carbon dioxide (CO2) than soils from the intact site during in vitro incubations. The response of CO2 production to changes in water-filled pore space (WFPS) followed a cubic polynomial relationship with maxima at 60–70% at the three sites. Methane (CH4) was produced in limited amounts and exclusively under water-saturated conditions. There was no significant response of nitrous oxide (N2O) emissions to WFPS variation. Lastly, the density of pneumatophore decreased drastically as the result of forest degradation and was positively correlated to in situ CH4 emissions. We conclude that recurrent M. flexuosa harvesting could result in a significant increase of in situ CO2 fluxes and a simultaneous decrease in CH4 emissions via pneumatophores. These changes might alter long-term carbon and GHG balances of the peat, and the role of these ecosystems for climate change mitigation, which stresses the need for their protection.
    Kinetic analysis of the influenza A virus HA/NA balance reveals contribution of NA to virus-receptor binding and NA-dependent rolling on receptor-containing surfaces
    Guo, Hongbo ; Rabouw, Huib ; Slomp, Anne ; Dai, Meiling ; Vegt, Floor van der; Lent, Jan W.M. van; McBride, Ryan ; Paulson, James C. ; Groot, Raoul J. de; Kuppeveld, Frank J.M. van; Vries, Erik de; Haan, Cornelis A.M. de - \ 2018
    PLoS Pathogens 14 (2018)8. - ISSN 1553-7366

    Interactions of influenza A virus (IAV) with sialic acid (SIA) receptors determine viral fitness and host tropism. Binding to mucus decoy receptors and receptors on epithelial host cells is determined by a receptor-binding hemagglutinin (HA), a receptor-destroying neuraminidase (NA) and a complex in vivo receptor-repertoire. The crucial but poorly understood dynamics of these multivalent virus-receptor interactions cannot be properly analyzed using equilibrium binding models and endpoint binding assays. In this study, the use of biolayer interferometric analysis revealed the virtually irreversible nature of IAV binding to surfaces coated with synthetic sialosides or engineered sialoglycoproteins in the absence of NA activity. In addition to HA, NA was shown to be able to contribute to the initial binding rate while catalytically active. Virus-receptor binding in turn contributed to receptor cleavage by NA. Multiple low-affinity HA-SIA interactions resulted in overall extremely high avidity but also permitted a dynamic binding mode, in which NA activity was driving rolling of virus particles over the receptor-surface. Virus dissociation only took place after receptor density of the complete receptor-surface was sufficiently decreased due to NA activity of rolling IAV particles. The results indicate that in vivo IAV particles, after landing on the mucus layer, reside continuously in a receptor-bound state while rolling through the mucus layer and over epithelial cell surfaces driven by the HA-NA-receptor balance. Quantitative BLI analysis enabled functional examination of this balance which governs this dynamic and motile interaction that is expected to be crucial for penetration of the mucus layer and subsequent infection of cells by IAV but likely also by other enveloped viruses carrying a receptor-destroying enzyme in addition to a receptor-binding protein.

    An advanced view on Baculovirus per Os infectivity factors
    Boogaard, Bob ; Oers, Monique M. van; Lent, Jan W.M. van - \ 2018
    Insects 9 (2018)3. - ISSN 2075-4450
    Baculovirus - Membrane fusion - ODV entry complex - ODV-E56 - ODV-E66 - Per os infectivity factors - Pif - Protein trafficking - R18 de-quenching assay

    Baculoviruses are arthropod-specific large DNA viruses that orally infect the larvae of lepidopteran, hymenopteran and dipteran insect species. These larvae become infected when they eat a food source that is contaminated with viral occlusion bodies (OBs). These OBs contain occlusion-derived viruses (ODVs), which are released upon ingestion of the OBs and infect the endothelial midgut cells. At least nine different ODV envelope proteins are essential for this oral infectivity and these are denoted per os infectivity factors (PIFs). Seven of these PIFs form a complex, consisting of PIF1, 2, 3 and 4 that form a stable core complex and PIF0 (P74), PIF6 and PIF8 (P95) that associate with this complex with lower affinity than the core components. The existence of a PIF complex and the fact that the pif genes are conserved in baculovirus genomes suggests that PIF-proteins cooperatively mediate oral infectivity rather than as individual functional entities. This review therefore discusses the knowledge obtained for individual PIFs in light of their relationship with other members of the PIF complex.

    Development of a Virosomal RSV Vaccine Containing 3D-PHAD® Adjuvant : Formulation, Composition, and Long-Term Stability
    Lederhofer, J. ; Lent, J. van; Bhoelan, F. ; Karneva, Z. ; Haan, A. de; Wilschut, J.C. ; Stegmann, T. - \ 2018
    Pharmaceutical Research 35 (2018)9. - ISSN 0724-8741
    adjuvant - monophosphoryl lipid A - respiratory syncytial virus - single particle tracking - vaccine - virosomes

    Purpose: Characterization of virosomes, in late stage preclinical development as vaccines for Respiratory Syncytial Virus (RSV), with a membrane-incorporated synthetic monophosphoryl lipid A, 3D-PHAD® adjuvant. Methods: Virosomes were initially formed by contacting a lipid film containing 3D-PHAD® with viral membranes solubilized with the short chain phospholipid DCPC, followed by dialysis, later by adding solubilized 3D-PHAD to viral membranes, or to preformed virosomes from DMSO. Results: Virosomes formed from lipid films contained the membrane glycoproteins G and F, at similar F to G ratios but lower concentrations than in virus, and the added lipids, but only a fraction of the 3D-PHAD®. By single particle tracking (SPT), the virosome size distribution resembled that seen by cryo-electron microscopy, but dynamic light scattering showed much larger particles. These differences were caused by small virosome aggregates. Measured by SPT, virosomes were stable for 300 days. 3DPHAD ® incorporation in virosomes could be enhanced by providing the adjuvant from DCPC solubilized stock, but also by adding DMSO dissolved adjuvant to pre-formed virosomes. Virosomes with 0.1 mg/mg of 3D-PHAD®/viral protein from DMSO induced antibody titers similar to those by virosomes containing 0.2 mg/mg of DCPC-solubilized 3D-PHAD®. Conclusions: Stable 3D-PHAD® adjuvanted RSV virosomes can be formulated.

    Baculoviruses require an intact ODV entry-complex to resist proteolytic degradation of per os infectivity factors by co-occluded proteases from the larval host
    Boogaard, Bob ; Lent, Jan W.M. Van; Theilmann, David A. ; Erlandson, Martin A. ; Oers, Monique M. van - \ 2017
    Journal of General Virology 98 (2017)12. - ISSN 0022-1317 - p. 3101 - 3110.
    AcMNPV - Co-occluded protease - Oral infectivity - Per os infectivity factor - PIF-comples - PIF6
    Baculoviruses orally infect caterpillars in the form of occlusion-derived viruses (ODVs). The ODV-envelope contains a number of proteins which are essential for oral infectivity, called per os infectivity factors (PIFs). Most of these PIFs are involved in the formation of an ODV-entry complex that consists of a stable core, formed by PIF1, PIF2, PIF3 and PIF4, and the more loosely associated PIFs P74 (PIF0) and P95 (PIF8). PIF1, PIF2 and PIF3 are essential for formation of the stable core, whereas deletion of the pif4 gene results in the formation of a smaller complex. P74 is not needed for formation of the stable core. We show here in larva-derived ODVs of the Autographa californica multicapsid nucleopolyhedrovirus that PIF-proteins are degraded by host-derived proteases after deletion of a single pif-gene. Constituents of the stable core-complex appeared to be more resistant to proteases as part of the complex than as monomer, as in ODVs of a p74 deletion mutant only the stable core was found but no PIF monomers. When the stable core lacks PIF4, it lost its proteolytic resistance as the resulting smaller core complex was degraded in a pif4 deletion mutant. We also identified PIF6 as a loosely associated component of the entry complex that appeared nevertheless important for the proteolytic resistance of the stable core, which was degraded after deletion of pif6. We conclude from these results that an intact entry-complex in the ODV-envelope is prerequisite for proteolytic resistance of PIF-proteins under the alkaline conditions of the larval midgut.
    Identification of sialic acid-binding function for the Middle East respiratory syndrome coronavirus spike glycoprotein
    Li, Wentao ; Hulswit, Ruben J.G. ; Widjaja, Ivy ; Raj, V.S. ; McBride, Ryan ; Peng, Wenjie ; Widagdo, W. ; Tortorici, M.A. ; Dieren, Brenda van; Lang, Yifei ; Lent, Jan W.M. van; Paulson, James C. ; Haan, Cornelis A.M. de; Groot, Raoul J. de; Kuppeveld, Frank J.M. Van; Haagmans, Bart L. ; Bosch, Berend-Jan - \ 2017
    Proceedings of the National Academy of Sciences of the United States of America 114 (2017)40. - ISSN 0027-8424 - p. E8508 - E8517.
    Attachment - MERS-CoV - Receptor - Sialic acid - Spike

    Middle East respiratory syndrome coronavirus (MERS-CoV) targets the epithelial cells of the respiratory tract both in humans and in its natural host, the dromedary camel. Virion attachment to host cells is mediated by 20-nm-long homotrimers of spike envelope protein S. The N-terminal subunit of each S protomer, called S1, folds into four distinct domains designated S1A through S1D. Binding of MERS-CoV to the cell surface entry receptor dipeptidyl peptidase 4 (DPP4) occurs via S1B. We now demonstrate that in addition to DPP4, MERS-CoV binds to sialic acid (Sia). Initially demonstrated by hemagglutination assay with human erythrocytes and intact virus, MERS-CoV Sia-binding activity was assigned to S subdomain S1A. When multivalently displayed on nanoparticles, S1 or S1A bound to human erythrocytes and to human mucin in a strictly Sia-dependent fashion. Glycan array analysis revealed a preference for α2,3-linked Sias over α2,6-linked Sias, which correlates with the differential distribution of α2,3-linked Sias and the predominant sites of MERS-CoV replication in the upper and lower respiratory tracts of camels and humans, respectively. Binding is hampered by Sia modifications such as 5-N-glycolylation and (7,)9-O-acetylation. Depletion of cell surface Sia by neuraminidase treatment inhibited MERS-CoV entry of Calu-3 human airway cells, thus providing direct evidence that virus–Sia interactions may aid in virion attachment. The combined observations lead us to propose that high-specificity, low-affinity attachment of MERS-CoV to sialoglycans during the preattachment or early attachment phase may form another determinant governing the host range and tissue tropism of this zoonotic pathogen.

    Supramolecular Virus-Like Nanorods by Coassembly of a Triblock Polypeptide and Reversible Coordination Polymers
    Hernandez-Garcia, Armando ; Velders, Aldrik H. ; Cohen Stuart, Martien ; Vries, Renko de; Lent, Jan van; Wang, Junyou - \ 2017
    Chemistry-A European Journal 23 (2017)2. - ISSN 0947-6539 - p. 239 - 243.
    Coordination polymers - Hybrid nanomaterials - Polypeptides - Protein engineering - Self-assembly

    We investigate a new case of a self-assembly-stimulated self-assembly in which a triblock polypeptide is combined with a anionic coordination polymer of a dipicolinic acid bis-ligand, and d- or f- block metal ions like ZnII or EuIII. The polypeptide not only has a silk-like domain that can fold and stack, but also a C-terminal cationic sequence by which it can interact with the supramolecular (coordination) polyanion. In the presence of all three ingredients (polypeptide, bis-ligand, and metal ions), we observe the initiation and slow growth of well-defined metal-containing nanorods of up to 150nm in length, proving that self-assembly of the polypeptide is triggered by the self-assembly of the coordination polyelectrolyte and vice versa. The particles, which have a striking resemblance to rod-like viruses, are stable up to 1.2m NaCl, and can be made fluorescent when lanthanides like EuIII are used, showing the potential to exploit functional properties and applications of virus-like supramolecular structures.

    Baculovirus midgut entry: the role of per os infectivity factors (PIFs)
    Oers, M.M. van; Peng, Ke ; Boeren, J.A. ; Mu, Jingfang ; Boogaard, Bob ; Vlak, J.M. ; Lent, J.W.M. van - \ 2016
    Baculoviruses infect insect midgut epithelial cells in the form of occlusion-derived virus (ODVs) particles..For Autographa californica multiple nucleopolyhedrovirus (AcMNPV) at least seven conserved ODV membrane proteins are essential for oral infectivity. These proteins are called per os infectivity factors (PIFs). We identified a multi-molecular complex composed of PIF1, PIF2, PIF3, and PIF4. Co-immunoprecipitation (CoIP) combined with proteomic analysis was used to identify other components of the AcMNPV PIF complex. Differentially denaturing SDS-PAGE further confirmed that PIF4 forms a stable complex with PIF1, PIF2, and PIF3. Deletion of the genes for either PIF1, PIF2, PIF3, or PIF4 impaired complex formation, but absence of P74 or PIF5 did not, in line with the fact that P74 was more loosely associated with the complex and PIF 5 was not found in the complex. CO-IP indicated that PIF-6 is also associated with the PIF complex, as well as three other proteins P95, AC5 and AC!08. To monitor the entry of virus into primary midgut epithelium cells in detail we constructed a baculovirus with EGFP fused to the VP939 nucleocapsid protein. This allowed us to study the ability to bind and enter host cells ex vivo using confocal fluorescence microscopy. When applied to wild type AcMNPV and viruses with mutations in P74 (PIF0), PIF1 or PIF2, it was shown that P74 is required for ODV binding. Viruses with PIF1 and PIF2 deletions still bound to midgut epithelial cells but were not able to enter. The live imaging of ODV entry into midgut cells complements the genetic and biochemical evidence for the role of PIFs in the oral infection process.
    Genetically manipulated phages with improved pH resistance for oral administration in veterinary medicine
    Nobrega, Franklin L. ; Costa, Ana Rita ; Santos, José F. ; Siliakus, Melvin F. ; Lent, Jan W.M. Van; Kengen, Servé W.M. ; Azeredo, Joana ; Kluskens, Leon D. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322
    Orally administered phages to control zoonotic pathogens face important challenges, mainly related to the hostile conditions found in the gastrointestinal tract (GIT). These include temperature, salinity and primarily pH, which is exceptionally low in certain compartments. Phage survival under these conditions can be jeopardized and undermine treatment. Strategies like encapsulation have been attempted with relative success, but are typically complex and require several optimization steps. Here we report a simple and efficient alternative, consisting in the genetic engineering of phages to display lipids on their surfaces. Escherichia coli phage T7 was used as a model and the E. coli PhoE signal peptide was genetically fused to its major capsid protein (10 A), enabling phospholipid attachment to the phage capsid. The presence of phospholipids on the mutant phages was confirmed by High Performance Thin Layer Chromatography, Dynamic Light Scattering and phospholipase assays. The stability of phages was analysed in simulated GIT conditions, demonstrating improved stability of the mutant phages with survival rates 102-107 pfu.mL-1 higher than wild-type phages. Our work demonstrates that phage engineering can be a good strategy to improve phage tolerance to GIT conditions, having promising application for oral administration in veterinary medicine.
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