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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Validating the demethylating effects of 5-aza-20-deoxycytidine in insects requires a whole-genome approach (A reply to ellers et al.)
Cook, Nicola ; Parker, Darren J. ; Tauber, Eran ; Pannebakker, Bart A. ; Shuker, David M. - \ 2019
American Naturalist 194 (2019)3. - ISSN 0003-0147 - p. 432 - 438.
5-aza-2-deoxycytidine - DNA methylation - Nasonia vitripennis - Sex ratio

We previously demonstrated that treatment with the de-methylating agent 5-aza-20-deoxycytidine (5-aza-dC) alters the offspring sex ratios produced by females of the parasitoid wasp Nasonia vitripennis. Females allocate offspring sex ratio in line with local mate competition theory, producing more or less female-biased sex ratios as the number of other females laying eggs on a patch varies, thereby reducing competition among their sons for mates. Interestingly, treatment with 5-aza-dC did not ablate the facultative sex allocation re-sponse. Instead, sex ratios became less female biased, a shift in the direction of the optimum sex ratio for paternally inherited alleles ac-cording to genomic conflict theory. This was the first (albeit indirect) experimental evidence for genomic conflict over sex allocation. In their comment, Ellers and colleagues assayed the effects of 5-aza-dC on DNA methylation in 10 Nasonia genes, finding no evidence of demeth-ylation in these 10 genes, from which they conclude that 5-aza-dC has no demethylating capability in N. vitripennis. Quantifying the efficacy of 5-aza-dC in terms of demethylation is indeed crucial to in-depth interpretation of studies using 5-aza-dC to link phenotypes to epigenetic regulation. Here we outline the mode of action of 5-aza-dC and demonstrate that determining the efficacy of 5-aza-dC in insect systems requires a whole-genome approach.

A coevolved EDS1-SAG101-NRG1 module mediates cell death signaling by TIR-domain immune receptors
Lapin, Dmitry ; Kovacova, Viera ; Sun, Xinhua ; Dongus, Joram ; Bhandari, Deepak ; Born, Patrick von; Bautor, Jaqueline ; Guarneri, Nina ; Rzemieniewski, Jakub ; Stuttmann, Johannes ; Beyer, Andreas ; Parker, Jane E. - \ 2019
The Plant Cell (2019). - ISSN 1040-4651
Plant intracellular nucleotide-binding/leucine-rich repeat (NLR) immune receptors are activated by pathogen effectors to trigger host defenses and cell death. Toll-Interleukin1-receptor (TIR)-domain NLRs (TNLs) converge on the Enhanced Disease Susceptibility1 (EDS1) family of lipase-like proteins for all resistance outputs. In Arabidopsis TNL immunity, AtEDS1 heterodimers with Phytoalexin Deficient4 (AtPAD4) transcriptionally boost basal defense pathways. AtEDS1 uses the same surface to interact with PAD4-related Senescence-Associated Gene101 (AtSAG101), but the role of AtEDS1-AtSAG101 heterodimers was unclear. We show that AtEDS1-AtSAG101 function together with AtNRG1 coiled-coil domain helper NLRs as a coevolved TNL cell death signaling module. AtEDS1-AtSAG101-AtNRG1 cell death activity is transferable to the solanaceous species, Nicotiana benthamiana, and cannot be substituted by AtEDS1-AtPAD4 with AtNRG1 or AtEDS1-AtSAG101 with endogenous NbNRG1. Analysis of EDS1-family evolutionary rate variation and heterodimer structure-guided phenotyping of AtEDS1 variants or AtPAD4-AtSAG101 chimeras identify closely aligned ɑ-helical coil surfaces in the AtEDS1-AtSAG101 partner C-terminal domains that are necessary for TNL cell death signaling. Our data suggest that TNL-triggered cell death and pathogen growth restriction are determined by distinctive features of EDS1-SAG101 and EDS1-PAD4 complexes and that these signaling machineries coevolved with further components within plant species or clades to regulate downstream pathways in TNL immunity.
Heet en niet te blussen : Conflicten als performatieve communicatiesystemen, een Luhmanniaans perspectief
Pellis, A. ; Duineveld, M. ; Vries, Jasper de - \ 2019
Tijdschrift voor Communicatiewetenschap 47 (2019)2. - ISSN 1384-6930 - p. 104 - 104.
Er is veel geschreven over conflicten en de wijze waarop we ze kunnen voorkomen, temperen of in goede banen kunnen leiden (zie o.a. Parker Follett, 1942; Mastenbroek, 1993; Aarts, Steuten & Van Woerkum, 2014; Glasl, 2015). In de gangbare benadering worden conflicten met name geobserveerd middels een diagnose-behandelcombinatie waarbinnen gezocht wordt naar de oorzaken en gevolgen van conflicten, en consistent wordt uitgegaan van een onderscheid tussen veroorzakers en conflictobjecten. De veroorzakers zijn dan twee of meer actoren (mensen, organisaties, staten, etc.) en het conflictobject kan van alles en nog wat zijn: landsgrenzen, kapitaal, natuurlijke hulpbronnen, of de kleur van de gordijnen in een nieuw huis. Als conflicten worden gezien als het resultaat van relaties tussen twee of meer actoren die een onenigheid hebben over bepaalde conflictobjecten, dan is het geen verrassing dat de focus van onderzoek en de daaruit voortkomende aanbevelingen voor interventie zich van oudsher op de veroorzakers, hun relaties en de conflictobjecten richt. Uit dergelijk onderzoek concludeert men dat er bemiddeld moet worden tussen twee partijen, en/of dat er iets gedaan moet worden aan de conflictobjecten; zoals het verstevigen van grenzen, het eerlijker verdelen van kapitaal, het vermijden van het gebruik van bepaalde hulpbronnen of het sluiten van een compromis over de kleur van de gordijnen.
Patterns of nitrogen-fixing tree abundance in forests across Asia and America
Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
Journal of Ecology (2019). - ISSN 0022-0477
forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal
Groenenboom, Anneloes E. ; Parker, Megan E. ; Vries, Anne De; Groot, Suzette de; Zobrist, Stephanie ; Mansen, Kimberly ; Milani, Peiman ; Kort, Remco ; Smid, Eddy J. ; Schoustra, Sijmen E. - \ 2019
PLoS ONE 14 (2019)5. - ISSN 1932-6203
Spontaneously fermented food products contain a complex, natural microbial community with potential probiotic activity. The addition of a health-promoting, probiotic bacterium to these products ensures the delivery of that probiotic activity to consumers. Here, we assess the microbial community of a traditional Senegalese milk product produced by spontaneous fermentation, called lait caillé. We produced the lait caillé in a traditional way and added a probiotic starter containing Lactobacillus rhamnosus yoba 2012 to the traditional process. We found various species that are known for their ability to ferment milk, including species from the genera Lactobacillus, Acetobacter, Lactococcus, and Streptococcus. Our results show that the addition of L. rhamnosus to the inoculum, can result in detectable levels of this strain in the final product, ranging between 0.2 and 1 percent of the total bacterial population. Subsequent rounds of fermentation using passive back-slopping without the addition of new L. rhamnosus led to a loss of this strain from the community of fermenting bacteria. Our results suggest that the addition of probiotic strains at every fermentation cycle can enrich the existing complex communities of traditionally fermented lait caillé while traditional bacterial strains remain dominant in the bacterial communities
Comparison of mechanical disturbance in soft sediments due to tickler-chain SumWing trawl vs. electro-fitted PulseWing trawl
Depestele, Jochen ; Degrendele, Koen ; Esmaeili, Moosa ; Ivanović, Ana ; Kröger, Silke ; O’neill, Finbarr G. ; Parker, Ruth ; Polet, Hans ; Roche, Marc ; Teal, Lorna R. ; Vanelslander, Bart ; Rijnsdorp, Adriaan D. - \ 2019
ICES Journal of Marine Science 76 (2019)1. - ISSN 1054-3139 - p. 312 - 329.
beam trawl - biogeochemistry - habitat impacts - Particle size distribution - penetration depth - pulse trawl - seafloor integrity - sediment resuspension
Tickler-chain SumWing and electrode-fitted PulseWing trawls were compared to assess seabed impacts. Multi-beam echo sounder (MBES) bathymetry confirmed that the SumWing trawl tracks were consistently and uniformly deepened to 1.5 cm depth in contrast to 0.7 cm following PulseWing trawling. MBES backscatter strength analysis showed that SumWing trawls (3.11 dB) flattened seabed roughness significantly more than PulseWing trawls (2.37 dB). Sediment Profile Imagery (SPI) showed that SumWing trawls (mean, SD) homogenised the sediment
deeper (3.4 cm, 0.9 cm) and removed more of the oxidised layer than PulseWing trawls (1 cm, 0.8 cm). The reduced PulseWing trawling impacts allowed a faster re-establishment of the oxidised layer and micro-topography. Particle size analysis suggested that SumWing trawls injected finer particles into the deeper sediment layers (4 cm depth), while PulseWing trawling only caused coarsening of the top layers (winnowing effect). Total penetration depth (mean, SD) of the SumWing trawls (4.1 cm, 0.9 cm) and PulseWing trawls (1.8 cm, 0.8 cm) was
estimated by the depth of the disturbance layer and the layer of mobilized sediment (SumWing ¼ 0.7 cm; PulseWing trawl ¼ 0.8 cm). PulseWing trawls reduced most of the mechanical seabed impacts compared to SumWing trawls for this substrate and area characteristics.
Hytrosavirus genetic diversity and eco-regional spread in Glossina species
Meki, Irene K. ; Kariithi, Henry M. ; Ahmadi, Mehrdad ; Parker, Andrew G. ; Vreysen, Marc J.B. ; Vlak, Just M. ; Oers, Monique M. van; Abd-Alla, Adly M.M. - \ 2018
BMC Microbiology 18 (2018). - ISSN 1471-2180
Genetic diversity - Glossinidae - GpSGHV - Haplotype - Salivary gland hypertrophy virus - Sterile insect technique - Tsetse - Virus evolution

BACKGROUND: The management of the tsetse species Glossina pallidipes (Diptera; Glossinidae) in Africa by the sterile insect technique (SIT) has been hindered by infections of G. pallidipes production colonies with Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae family). This virus can significantly decrease productivity of the G. pallidipes colonies. Here, we used three highly diverged genes and two variable number tandem repeat regions (VNTRs) of the GpSGHV genome to identify the viral haplotypes in seven Glossina species obtained from 29 African locations and determine their phylogenetic relatedness. RESULTS: GpSGHV was detected in all analysed Glossina species using PCR. The highest GpSGHV prevalence was found in G. pallidipes colonized at FAO/IAEA Insect Pest Control Laboratory (IPCL) that originated from Uganda (100%) and Tanzania (88%), and a lower prevalence in G. morsitans morsitans from Tanzania (58%) and Zimbabwe (20%). Whereas GpSGHV was detected in 25-40% of G. fuscipes fuscipes in eastern Uganda, the virus was not detected in specimens of neighboring western Kenya. Most of the identified 15 haplotypes were restricted to specific Glossina species in distinct locations. Seven haplotypes were found exclusively in G. pallidipes. The reference haplotype H1 (GpSGHV-Uga; Ugandan strain) was the most widely distributed, but was not found in G. swynnertoni GpSGHV. The 15 haplotypes clustered into three distinct phylogenetic clades, the largest contained seven haplotypes, which were detected in six Glossina species. The G. pallidipes-infecting haplotypes H10, H11 and H12 (from Kenya) clustered with H7 (from Ethiopia), which presumably corresponds to the recently sequenced GpSGHV-Eth (Ethiopian) strain. These four haplotypes diverged the most from the reference H1 (GpSGHV-Uga). Haplotypes H1, H5 and H14 formed three main genealogy hubs, potentially representing the ancestors of the 15 haplotypes. CONCLUSION: These data identify G. pallidipes as a significant driver for the generation and diversity of GpSGHV variants. This information may provide control guidance when new tsetse colonies are established and hence, for improved management of the virus in tsetse rearing facilities that maintain multiple Glossina species.

RNA interference-based antiviral immune response against the salivary gland hypertrophy virus in Glossina pallidipes
Meki, Irene K. ; Kariithi, Henry M. ; Parker, Andrew G. ; Vreysen, Marc J.B. ; Ros, Vera I.D. ; Vlak, Just M. ; Oers, Monique M. van; Abd-Alla, Adly M.M. - \ 2018
BMC Microbiology 18 (2018). - ISSN 1471-2180 - p. 257 - 270.
Covert infections - Glossinidae - GpSGHV - RNAi - Sterile insect technique - Symptomatic and asymptomatic infection - Tsetse

BACKGROUND: Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae) is a non-occluded dsDNA virus that specifically infects the adult stages of the hematophagous tsetse flies (Glossina species, Diptera: Glossinidae). GpSGHV infections are usually asymptomatic, but unknown factors can result to a switch to acute symptomatic infection, which is characterized by the salivary gland hypertrophy (SGH) syndrome associated with decreased fecundity that can ultimately lead to a colony collapse. It is uncertain how GpSGHV is maintained amongst Glossina spp. populations but RNA interference (RNAi) machinery, a conserved antiviral defense in insects, is hypothesized to be amongst the host's mechanisms to maintain the GpSGHV in asymptomatic (persistent or latent) infection state. Here, we investigated the involvement of RNAi during GpSGHV infections by comparing the expression of three key RNAi machinery genes, Dicer (DCR), Argonaute (AGO) and Drosha, in artificially virus injected, asymptomatic and symptomatic infected G. pallidipes flies compared to PBS injected (controls) individuals. We further assessed the impact of AGO2 knockdown on virus infection by RT-qPCR quantification of four selected GpSGHV genes, i.e. odv-e66, dnapol, maltodextrin glycosyltransferase (a tegument gene) and SGHV091 (a capsid gene). RESULTS: We show that in response to hemocoelic injections of GpSGHV into G. pallidipes flies, increased virus replication was accompanied by significant upregulation of the expression of three RNAi key genes; AGO1, AGO2 and DCR2, and a moderate increase in the expression of Drosha post injection compared to the PBS-injected controls. Furthermore, compared to asymptomatically infected individuals, symptomatic flies showed significant downregulation of AGO1, AGO2 and Drosha, but a moderate increase in the expression of DCR2. Compared to the controls, knockdown of AGO2 did not have a significant impact on virus infection in the flies as evidenced by unaltered transcript levels of the selected GpSGHV genes. CONCLUSION: The upregulation of the expression of the RNAi genes implicate involvement of this machinery in controlling GpSGHV infections and the establishment of symptomatic GpSGHV infections in Glossina. These findings provide a strategic foundation to understand GpSGHV infections and to control latent (asymptomatic) infections in Glossina spp. and thereby control SGHVs in insect production facilities.

A Summary of Research Activities from the AgMIP Potato Crop Modeling Intercomparison Pilot
Fleisher, D.H. ; Condori, B. ; Quiroz, R. ; Alva, A. ; Asseng, S. ; Barreda, Carolina ; Berghuijs, H.N.C. ; Bindi, M. ; Boote, K.J. ; Craigon, J. ; Fangmeier, A. ; Ferrise, Roberto ; Franke, A.C. ; Gayler, S. ; Govindakrishnan, P.M. ; Harahagazwe, Dieudonne ; Hoogenboom, G. ; Kremer, P. ; Kroes, J. ; Naresh Kumar, S. ; Merante, Paolo ; Nendel, C. ; Olesen, J.E. ; Parker, P.S. ; Pleijel, H. ; Raes, Dirk ; Raymundo, Rubi ; Reidsma, P. ; Ruana, A. ; Silva, J.V. ; Stella, T. ; Stockle, Claudio ; Supit, I. ; Evert, F.K. van; Vandermeiren, K. ; Vanuytrecht, Eline ; Vorne, V. ; Wolf, J. ; Woli, Prem - \ 2018
Activity-1 of the potato crop model intercomparison pilot was recently completed and focused on quantifying multi-model uncertainty to climate responses when using common data sets from low-and high-input management sites. Median model ensemble response outperformed any single model in terms of replicatingobserved yield across all sites. Uncertainty among models averaged 15% higher for low-versus high-input sites, with larger differences observed for evapotranspiration (ET), nitrogen uptake, and water use efficiency as compared to dry matter. A minimum of five partial, or three full, calibrated models was required for an ensemble approach to keep variability below that of common field variation. Model variation was not influenced by carbon dioxide (C), but increased as much as 41 and 23% for yield and ET respectively as temperature (T) or rainfall (W) moved away from historical levels. Increases in T accounted for the highest amount of uncertainty, suggesting that methods and parameters for T sensitivity represent a considerable unknown among models. Activity-2 research is on-going and tests the capability of multiple models to mimic effects of elevated C concentration on potato yields measured at eight different locations in Europe. A subset from observed OTC and FACE data was used to initially calibrate the models. This research will also evaluate the stability of the models’ calibration with respect to changes in geographic location, as the same variety was used in all locations. This presentation will summarize the Activity-1 results and discuss the current status of Activity-2 investigations.
Tropical land carbon cycle responses to 2015/16 El Niño as recorded by atmospheric greenhouse gas and remote sensing data
Gloor, Emanuel ; Wilson, Chris ; Chipperfield, Martyn P. ; Chevallier, Frederic ; Buermann, Wolfgang ; Boesch, Hartmut ; Parker, Robert ; Somkuti, Peter ; Gatti, Luciana V. ; Correia, Caio ; Domingues, Lucas G. ; Peters, Wouter ; Miller, John ; Deeter, Merritt N. ; Sullivan, Martin J.P. - \ 2018
Philosophical Transactions of the Royal Society B. Biological sciences 373 (2018)1760. - ISSN 0962-8436 - 12 p.
carbon cycle - fire - global warming - tropical forests

The outstanding tropical land climate characteristic over the past decades is rapid warming, with no significant large-scale precipitation trends. This warming is expected to continue but the effects on tropical vegetation are unknown. El Niño-related heat peaks may provide a test bed for a future hotter world. Here we analyse tropical land carbon cycle responses to the 2015/16 El Niño heat and drought anomalies using an atmospheric transport inversion. Based on the global atmospheric CO2 and fossil fuel emission records, we find no obvious signs of anomalously large carbon release compared with earlier El Niño events, suggesting resilience of tropical vegetation. We find roughly equal net carbon release anomalies from Amazonia and tropical Africa, approximately 0.5 PgC each, and smaller carbon release anomalies from tropical East Asia and southern Africa. Atmospheric CO anomalies reveal substantial fire carbon release from tropical East Asia peaking in October 2015 while fires contribute only a minor amount to the Amazonian carbon flux anomaly. Anomalously large Amazonian carbon flux release is consistent with downregulation of primary productivity during peak negative near-surface water anomaly (October 2015 to March 2016) as diagnosed by solar-induced fluorescence. Finally, we find an unexpected anomalous positive flux to the atmosphere from tropical Africa early in 2016, coincident with substantial CO release.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Expression profile of Glossina pallidipes MicroRNAs during symptomatic and asymptomatic infection with Glossina pallidipes salivary gland hypertrophy virus (Hytrosavirus)
Meki, Irene K. ; Ince, Ikbal A. ; Kariithi, Henry M. ; Boucias, Drion G. ; Ozcan, Orhan ; Parker, Andrew G. ; Vlak, Just M. ; Oers, Monique M. van; Abd-Alla, Adly M.M. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X
Asymptomatic infection - Glossina - GpSGHV - Hytrosaviridae - Immune system - MiRNA - Sterile insect technique - Symptomatic

The Glossina pallidipes salivary gland hypertrophy virus (GpSGHV) infects tsetse flies predominantly asymptomatically and occasionally symptomatically. Symptomatic infections are characterized by overt salivary gland hypertrophy (SGH) in mass reared tsetse flies, which causes reproductive dysfunctions and colony collapse, thus hindering tsetse control via sterile insect technique (SIT). Asymptomatic infections have no apparent cost to the fly's fitness. Here, small RNAs were sequenced and profiles in asymptomatically and symptomatically infected G. pallidipes flies determined. Thirty-eight host-encoded microRNAs (miRNAs) were present in both the asymptomatic and symptomatic fly profiles, while nine host miRNAs were expressed specifically in asymptomatic flies versus 10 in symptomatic flies. Of the shared 38 miRNAs, 15 were differentially expressed when comparing asymptomatic with symptomatic flies. The most up-regulated host miRNAs in symptomatic flies was predicted to target immune-related mRNAs of the host. Six GpSGHV-encoded miRNAs were identified, of which five of them were only in symptomatic flies. These virus-encoded miRNAs may not only target host immune genes but may also participate in viral immune evasion. This evidence of differential host miRNA profile in Glossina in symptomatic flies advances our understanding of the GpSGHV-Glossina interactions and provides potential new avenues, for instance by utilization of particular miRNA inhibitors or mimics to better manage GpSGHV infections in tsetse mass-rearing facilities, a prerequisite for successful SIT implementation.

Habitats impacts by beam and pulse trawling in the Southern North Sea
Depestele, Jochen ; Degrendele, Koen ; Esmaeili, Moosa ; Ivanovic, Ana ; Kroger, Silke ; O'Neill, Finbarr G. ; Parker, Ruth ; Polet, Hans ; Roche, Marc ; Summerbell, Keith ; Teal, L.R. ; Vanelslander, Bart ; Rijnsdorp, A.D. - \ 2018
- 17 p.
Mechanical seabed disturbance by flatfish-directed tickler-chain trawls and pulse trawls
Depestele, Jochen ; Degrendele, Koen ; Esmaeili, Moosa ; Ivanovic, Ana ; Kroger, Silke ; O'Neill, Finbarr G. ; Parker, Ruth ; Polet, Hans ; Roche, Marc ; Summerbell, Keith ; Teal, L.R. ; Vanelslander, Bart ; Rijnsdorp, A.D. - \ 2018
Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; Diatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephen C.J. ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723 - 1 p.

A correction to this article has been published and is linked from the HTML version of this article.

Planning and governance issues in the restructuring of the high street
Peel, Deborah ; Parker, Cathy - \ 2017
Journal of Place Management and Development 10 (2017)4. - ISSN 1753-8335 - p. 404 - 418.
Governance - Holistic - Joint working - Resilience - Restructuring - Wicked issue

Purpose: This paper aims to examine the role of “restructuring” in confronting the challenges facing contemporary high streets in the devolved UK. It complements three articles concerned with repositioning, reinventing and rebranding and illustrates the multi-faceted approaches involved in addressing retail change and town centre transformations. This paper emphasises the role of planning and governance in effecting change. Design/methodology/approach: Informed by a literature review, action research involved inter-related interventions in selected locations, and associated workshops with engaged practitioners and community actors. Findings: The findings highlight that the “resilience” of contemporary town centres demands resisting efforts to return to the status quo and necessitate forms of adaptive management. Understanding high street degeneration and the limitations of a retail-only led policy focus as a “wicked issue” further demands socially constructing town centres as an ecosystem requiring a holistic response. New forms of joint-working involve selecting appropriate models, attending to relational aspects and defined roles and responsibilities. Land use planning, including masterplanning and creating evidenced policy options, provides an important democratic space for legitimising action, offering leadership and extending participation to new change agents. Practical implications: Restructuring of governance is an essential prerequisite in effecting change. Originality/value: The originality of this study lies in the application of the restructuring element of the 4 Rs Framework which enables a focus on the governance dimensions of town centre and high street regeneration. The findings are enhanced through the experiential evidence which stresses both the importance of place-based diversification and value of prioritising holistic and joint actions developed through participatory visioning exercises.

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
Preface : Focus on imaging methods in granular physics
Amon, Axelle ; Born, Philip ; Daniels, Karen E. ; Dijksman, Joshua A. ; Huang, Kai ; Parker, David ; Schröter, Matthias ; Stannarius, Ralf ; Wierschem, Andreas - \ 2017
Review of Scientific Instruments 88 (2017)5. - ISSN 0034-6748
A potato model intercomparison across varying climates and productivity levels
Fleisher, David H. ; Condori, Bruno ; Quiroz, Roberto ; Alva, Ashok ; Asseng, Senthold ; Barreda, Carolina ; Bindi, Marco ; Boote, Kenneth J. ; Ferrise, Roberto ; Franke, Angelinus C. ; Govindakrishnan, Panamanna M. ; Harahagazwe, Dieudonne ; Hoogenboom, Gerrit ; Naresh Kumar, Soora ; Merante, Paolo ; Nendel, Claas ; Olesen, Jorgen E. ; Parker, Phillip S. ; Raes, Dirk ; Raymundo, Rubi ; Ruane, Alex C. ; Stockle, Claudio ; Supit, Iwan ; Vanuytrecht, Eline ; Wolf, Joost ; Woli, Prem - \ 2017
Global Change Biology 23 (2017)3. - ISSN 1354-1013 - p. 1258 - 1281.
A potato crop multimodel assessment was conducted to quantify variation among models and evaluate responses to climate change. Nine modeling groups simulated agronomic and climatic responses at low-input (Chinoli, Bolivia and Gisozi, Burundi)- and high-input (Jyndevad, Denmark and Washington, United States) management sites. Two calibration stages were explored, partial (P1), where experimental dry matter data were not provided, and full (P2). The median model ensemble response outperformed any single model in terms of replicating observed yield across all locations. Uncertainty in simulated yield decreased from 38% to 20% between P1 and P2. Model uncertainty increased with interannual variability, and predictions for all agronomic variables were significantly different from one model to another (P < 0.001). Uncertainty averaged 15% higher for low- vs. high-input sites, with larger differences observed for evapotranspiration (ET), nitrogen uptake, and water use efficiency as compared to dry matter. A minimum of five partial, or three full, calibrated models was required for an ensemble approach to keep variability below that of common field variation. Model variation was not influenced by change in carbon dioxide (C), but increased as much as 41% and 23% for yield and ET, respectively, as temperature (T) or rainfall (W) moved away from historical levels. Increases in T accounted for the highest amount of uncertainty, suggesting that methods and parameters for T sensitivity represent a considerable unknown among models. Using median model ensemble values, yield increased on average 6% per 100-ppm C, declined 4.6% per °C, and declined 2% for every 10% decrease in rainfall (for nonirrigated sites). Differences in predictions due to model representation of light utilization were significant (P < 0.01). These are the first reported results quantifying uncertainty for tuber/root crops and suggest modeling assessments of climate change impact on potato may be improved using an ensemble approach.
Cognitive performance and iron status are negatively associated with hookworm infection in Cambodian schoolchildren
Kuong, Khov ; Fiorentino, Marion ; Perignon, Marlene ; Chamnan, Chhoun ; Berger, Jacques ; Sinuon, Muth ; Molyden, Vann ; Burja, Kurt ; Parker, Megan ; Ly, Sou Chheng ; Friis, Henrik ; Roos, Nanna ; Wieringa, Frank T. - \ 2016
American Journal of Tropical Medicine and Hygiene 95 (2016)4. - ISSN 0002-9637 - p. 856 - 863.

Soil-transmitted helminth (STH) infection has been associated with lower cognitive performance of schoolchildren. To identify pathways through which STH infection might affect school performance, baseline data from a large rice-fortification trial in Cambodian schoolchildren were used to investigate associations between STH infection, micronutrient status, anemia, and cognitive performance. Complete data on anthropometry, cognitive performance, and micronutrient status were available for 1,760 schoolchildren, 6-16 years of age. STH infection was identified using Kato-Katz, whereas cognitive performance was assessed using Raven's Colored Progressive Matrices (RCPM), block design, and picture completion. STH infection was found in 18% of the children; almost exclusively hookwork infection. After adjusting for age and gender, raw cognitive test scores were significantly lower in hookworminfected children (-0.65; -0.78; -2.03 points for picture completion, RCPM, and block design, respectively; P <0.05 for all). Hookworm infection was associated with iron status (total body iron), but not with vitamin A and zinc status, nor with inflammation or anthropometry. Body iron was negatively associated with increased intensity of hookworm infection (R = 0.22, P <0.001). Hookworm infection in Cambodian schoolchildren was associated with lower cognitive performance, an effect most likely mediated through lower body iron. Interventions that are more effective against hookworm infection are needed to contribute to better health and improvement of cognitive performance.

Public health adaptation to climate change in OECD countries
Austin, Stephanie E. ; Biesbroek, Robbert ; Berrang-Ford, Lea ; Ford, James D. ; Parker, Stephen ; Fleury, Manon D. - \ 2016
International Journal of Environmental Research and Public Health 13 (2016)9. - ISSN 1660-4601
Adaptation - Adaptation tracking - Climate change - OECD countries - Public health

Climate change is a major challenge facing public health. National governments play a key role in public health adaptation to climate change, but there are competing views on what responsibilities and obligations this will—or should—include in different nations. This study aims to: (1) examine how national-level public health adaptation is occurring in Organization for Economic Cooperation and Development (OECD) countries; (2) examine the roles national governments are taking in public health adaptation; and (3) critically appraise three key governance dimensions of national-level health adaptation—cross-sectoral collaboration, vertical coordination and national health adaptation planning—and identify practical examples suited to different contexts. We systematically reviewed publicly available public health adaptation to climate change documents and webpages by national governments in ten OECD countries using systematic web searches, assessment of self-reporting, and content analysis. Our findings suggest national governments are primarily addressing infectious disease and heat-related risks posed by climate change, typically emphasizing capacity building or information-based groundwork initiatives. We find national governments are taking a variety of approaches to public health adaptation to climate change that do not follow expected convergence and divergence by governance structure. We discuss practical options for incorporating cross-sectoral collaboration, vertical coordination and national health adaptation planning into a variety of contexts and identify leaders national governments can look to to inform their public health adaptation planning. Following the adoption of the Paris Agreement and subsequent increased momentum for adaptation, research tracking adaptation is needed to define what health adaptation looks like in practice, reveal insights that can be taken up across states and sectors, and ensure policy orientated learning.

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