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1.
Dieke Boezen Ghulam Ali Manli Wang Xi Wang Wopke van der Werf Just M. Vlak Mark P. Zwart 《PLoS genetics》2022,18(6)
Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Our results highlight that viral demography and the stringency of mutation calling affect mutation rate estimates, and that using a population genetic simulation model to make inferences can mitigate the impact of these processes on estimates of mutation rate. We estimated a mutation rate of μ = 1×10−7 s/n/r when applying the most stringent criteria for mutation calling, and estimates of up to μ = 5×10−7 s/n/r when relaxing these criteria. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed. 相似文献
2.
Shuangwei Li Jochem B. Evers Wopke van der Werf Ruili Wang Zhaoli Xu Yan Guo Baoguo Li Yuntao Ma 《The Annals of applied biology》2020,177(2):195-210
Maize/soybean strip intercropping is a commonly used system throughout China with high crop yields at reduced nutrient input compared to sole maize. Maize is the taller crop, and due to its dominance in light capture over soybean in the intercrop, maize is expected to outperform maize in sole cropping. Conversely, soybean is the subordinate crop and intercropped soybean plants are expected to perform worse than sole soybean. Crop plants show plastic responses in plant architecture to their growing conditions to forage for light and avoid shading. There is little knowledge on plant architectural responses to growing conditions in simultaneous (non-relay) intercropping and their relationship to species yields. A two-year field experiment with two simultaneous maize/soybean intercropping systems with narrow and wide strips was conducted to characterise architectural traits of maize and soybean plants grown as intercrop and sole crops. Intercropped maize plants, especially those in border rows, had substantially greater leaf area, biomass and yield than maize plants in sole crops. Intercropped soybean plants, especially those in border rows, had lower leaf area, biomass and yield than sole soybean plants. Overall intercrop performance was similar to that of sole crops, with the land equivalent ratio (LER) being only slightly greater than one (1.03–1.08). Soybean displayed typical shade avoidance responses in the intercrop, such as greater internode elongation and changes in specific leaf area, but these responses could not overcome the consequences of the competition with the taller maize plants. Therefore, in contrast to relay intercrop systems, in the studied simultaneous maize/soybean system, plastic responses did not contribute to practically relevant increases in resource capture and yield at whole system (i.e., intercrop) level. 相似文献
3.
John Michael Hardman Wopke van der Werf Suzanne E. Blatt Jeffrey L. Franklin Richard Karsten Holger Teismann 《Experimental & applied acarology》2013,60(2):181-203
Successful biological control of mites is possible under various conditions, and identifying what are the requirements for robust control poses a challenge because interacting factors are involved. Process-based modeling can help to explore these interactions and identify under which conditions biological control is likely, and when not. Here, we present a process-based model for population interactions between the phytophagous mite, Tetranychus urticae, and its predator, Typhlodromus pyri, on apple trees. Temperature and leaf nitrogen concentration influence T. urticae rates of development and reproduction, while temperature and rate of ingestion of prey and pollen influence T. pyri rates of survival and reproduction. Predator and prey population dynamics are linked through a stage structured functional response model that accounts for spatial heterogeneity in population density throughout the trees. T. urticae biomass-days (BMD’s), which account for sizes of larvae, nymphs and adults, indicate level of mite-induced leaf damage. When BMD’s exceed 290 per leaf, there are economic losses. When BMD’s exceed 350 per leaf, T. urticae population growth is curbed and eventually the population decreases. Simulations were run to determine which conditions would lead to current year economic loss and increased risk of loss in the following year, i.e. where more T. urticae than T. pyri are present at the end of September. Risk was high with one or more of the following initial conditions: a high prey: predator ratio (10:1 or more); a low to intermediate (0.04–0.2 T. urticae per leaf) initial density; T. urticae with a higher initial proportion of adult females than T. pyri; and a delayed first detection of mites, whether in late July, or sometimes in late June, but not in early June. Warm summer weather, higher leaf nitrogen and T. urticae immigration into trees were also risk factors. Causes for these patterns based on biological characteristics of T. urticae and T. pyri are discussed, as are counter measures which can be taken to reduce risk. 相似文献
4.
Liljana Georgievska Renate Velders Felix J.J.A. Bianchi Wopke van der Werf 《Journal of invertebrate pathology》2010,105(1):30-35
Competition between virus genotypes in insect hosts is a key element of virus fitness, affecting their long-term persistence in agro-ecosystems. Little information is available on virus competition in insect hosts or during serial passages from one cohort of hosts to the next. Here we report on the competition between two genotypes of Spodoptera exigua nucleopolyhedrovirus (SeMNPV), when serially passaged as mixtures in cohorts of 4th instar S. exigua larvae. One of the genotypes was a SeMNPV wild-type isolate, SeUS1, while the other was a SeMNPV recombinant (SeMNPV-XD1) having a greater speed of kill than SeUS1. SeXD1 lacks a suite of genes, including the ecdysteroid UDP-glucosyl transferase (egt) gene. SeXD1 expresses the green fluorescent protein (GFP) gene, enabling the identification of SeXD1 in cell culture and in insects. The relative proportion of SeUS1 and SeXD1 in successive passages of mixed infections in various ratios was determined by plaque assays of budded virus from infected larvae and by polymerase chain reactions and restriction enzyme analyses. The SeUS1 genotype outcompeted recombinant SeXD1 over successive passages. Depending on the initial virus genotype ratio, the recombinant SeXD1 was no longer detected after 6-12 passages. A mathematical model was developed to characterize the competition dynamics. Overall, the ratio SeUS1/XD1 increased by a factor 1.9 per passage. The findings suggest that under the experimental conditions recombinant SeXD1 is displaced by the wild-type strain SeUS1, but further studies are needed to ascertain that this is also the case when the same baculoviruses would be used in agro-ecosystems. 相似文献
5.
Liljana Georgievska Nina Joosten Kelli Hoover Jenny S. Cory Just M. Vlak Wopke Van Der Werf 《Entomologia Experimentalis et Applicata》2010,135(1):56-67
Naturally occurring insect viruses can modify the behaviour of infected insects and thereby modulate virus transmission. Modifications of the virus genome could alter these behavioural effects. We studied the distance moved and the position of virus‐killed cadavers of fourth instars of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) infected with a wild‐type genotype of H. armigera nucleopolyhedrovirus (HaSNPV) or with one of two recombinant genotypes of this virus on cotton plants. The behavioural effects of virus infection were examined both in larvae infected with a single virus genotype, and in larvae challenged with mixtures of the wild‐type and one of the recombinant viruses. An egt‐negative virus variant caused more rapid death and lower virus yield in fourth instars, but egt‐deletion did not produce consistent behavioural effects over three experiments, two under controlled glasshouse conditions and one in field cages. A recombinant virus containing the AaIT‐(Androctonus australis Hector) insect‐selective toxin gene, which expresses a neurotoxin derived from a scorpion, caused faster death and cadavers were found lower down the plant than insects infected with unmodified virus. Larvae that died from mixed infections of the AaIT‐expressing recombinant and the wild‐type virus died at positions significantly lower, compared to infection with the pure wild‐type viral strain. The results indicate that transmission of egt‐negative variants of HaSNPV are likely to be affected by lower virus yield, but not by behavioural effects of egt gene deletion. By contrast, the AaIT recombinant will produce lower virus yields as well as modified behaviour, which together can contribute to reduced virus transmission under field conditions. In addition, larvae infected with both the wild‐type virus and the toxin recombinant behaved as larvae infected with the toxin recombinant only, which might be a positive factor for the risk assessment of such toxin recombinants in the environment. 相似文献
6.
Framework for Modelling Economic Impacts of Invasive Species,Applied to Pine Wood Nematode in Europe
Tarek Soliman Monique C. M. Mourits Wopke van der Werf Geerten M. Hengeveld Christelle Robinet Alfons G. J. M. Oude Lansink 《PloS one》2012,7(9)
Background
Economic impact assessment of invasive species requires integration of information on pest entry, establishment and spread, valuation of assets at risk and market consequences at large spatial scales. Here we develop such a framework and demonstrate its application to the pinewood nematode, Bursaphelenchus xylophilus, which threatens the European forestry industry. The effect of spatial resolution on the assessment result is analysed.Methodology/Principal Findings
Direct economic impacts resulting from wood loss are computed using partial budgeting at regional scale, while impacts on social welfare are computed by a partial equilibrium analysis of the round wood market at EU scale. Substantial impacts in terms of infested stock are expected in Portugal, Spain, Southern France, and North West Italy but not elsewhere in EU in the near future. The cumulative value of lost forestry stock over a period of 22 years (2008–2030), assuming no regulatory control measures, is estimated at €22 billion. The greatest yearly loss of stock is expected to occur in the period 2014–2019, with a peak of three billion euros in 2016, but stabilizing afterwards at 300–800 million euros/year. The reduction in social welfare follows the loss of stock with considerable delay because the yearly harvest from the forest is only 1.8%. The reduction in social welfare for the downstream round wood market is estimated at €218 million in 2030, whereby consumers incur a welfare loss of €357 million, while producers experience a €139 million increase, due to higher wood prices. The societal impact is expected to extend to well beyond the time horizon of the analysis, and long after the invasion has stopped.Conclusions/Significance
Pinewood nematode has large economic consequences for the conifer forestry industry in the EU. A change in spatial resolution affected the calculated directed losses by 24%, but did not critically affect conclusions. 相似文献7.
Junqi Zhu Bruno Andrieu Jan Vos Wopke van der Werf Christian Fournier Jochem B. Evers 《Annals of botany》2014,114(4):753-762
Background and Aims
Experimental evidence challenges the approximation, central in crop models, that developmental events follow a fixed thermal time schedule, and indicates that leaf emergence events play a role in the timing of development. The objective of this study was to build a structural development model of maize (Zea mays) based on a set of coordination rules at organ level that regulate duration of elongation, and to show how the distribution of leaf sizes emerges from this.Methods
A model of maize development was constructed based on three coordination rules between leaf emergence events and the dynamics of organ extension. The model was parameterized with data from maize grown at a low plant population density and tested using data from maize grown at high population density.Key Results
The model gave a good account of the timing and duration of organ extension. By using initial conditions associated with high population density, the model reproduced well the increase in blade elongation duration and the delay in sheath extension in high-density populations compared with low-density populations. Predictions of the sizes of sheaths at high density were accurate, whereas predictions of the dynamics of blade length were accurate up to rank 9; moderate overestimation of blade length occurred at higher ranks.Conclusions
A set of simple rules for coordinated growth of organs is sufficient to simulate the development of maize plant structure without taking into account any regulation by assimilates. In this model, whole-plant architecture is shaped through initial conditions that feed a cascade of coordination events. 相似文献8.
Recently, a novel isolate of the baculovirus Spodoptera litura nucleopolyhedrovirus (SpltNPV) has been isolated from Pakistan, which is distinct from the type species SpltNPV-G2 (ICTV). Here, we examined the biological activity of this isolate (SpltNPV-Pak-BNG) in second (L2), third (L3) and fourth instar (L4) larvae of the leafworm S. litura, more specifically to measure biological properties that are relevant for use of this virus for pest control under field conditions. The median lethal dose for L2 and L3 instar larvae was similar, but significantly lower than for L4 larvae. Likewise, the survival time was similar for L2 and L3 larvae (84?h), but was significantly longer for L4 instar larvae (108?h). Thus, in terms of efficacy, S. litura L2 and L3 instar larvae are the preferred targets for S. litura control with SpltNPV-Pak-BNG in field crops in Pakistan. On the basis of our data spray regimes can be designed to control the leafworm in cotton and vegetable crops targeting L2 and L3 larvae. 相似文献
9.
Spodoptera litura is an emerging insect pest in a wide range of crops worldwide. The insect is difficult to control because of resistance development to synthetic insecticides and emerging resistance to Bacillus thuringiensis toxins. Therefore, there is a need to develop biological control agents, preferably from an indigenous source to avoid risks associated with the importation of exotic natural antagonists. A Pakistani isolate of S. litura nucleopolyhedrovirus (SpltNPV, Baculoviridae), SpltNPV-Pak-BNG, was obtained from the field and characterized biologically and genetically, and compared to a SpltNPV reference isolate, SpltNPV-G1, thought to be of Chinese origin. The dose–mortality response (LD50) of SpltNPV-Pak-BNG was not significantly different from that of the reference isolate SpltNPV-G1, but the time-to-death (LT50) was significantly shorter for SpltNPV-Pak-BNG than for SpltNPV-G1. DNA restriction enzyme profiling indicated that SpltNPV-Pak-BNG and SpltNPV-G1 are different viruses. Sequence analysis of ‘ORF24’, specific for SpltNPV (and S. littoralis NPV as ORF21), and the conserved baculovirus core genes polyhedrin, DNApol, pif-2 and lef-8 confirmed that this was indeed the case and that SpltNPV-Pak-BNG is a genuine SpltNPV variant, whereas the SpltNPV-G1 isolate we used is, in fact, a SpliNPV variant, renamed to SpliNPV-G1. The newly isolated SpltNPV-Pak-BNG has the potential for development as a biocontrol agent of S. litura in Pakistan. 相似文献
10.
Felix J. J. A. Bianchi Nina N. Joosten Just M. Vlak Wopke van der Werf 《Biological Control》2000,19(3):252
Dose– and time–mortality relationships of baculoviruses in pest insects are important for the determination of effective spraying regimes. A series of experiments with Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and Spodoptera exigua MNPV (SeMNPV) against synchronized populations of S. exigua larvae in greenhouse chrysanthemum was conducted. Dose– and time–mortality relationships of different virus concentrations and S. exigua target stages were determined and the area foliage consumption was measured. Crop injury was greatly reduced when S. exigua were controlled as second or third instar larvae, whereas virus applications against fourth instar larvae could not prevent considerable crop injury, even at high concentrations. SeMNPV was approximately 10 times as infectious as AcMNPV when applied on greenhouse chrysanthemum. The relative virulence of AcMNPV and SeMNPV corresponded reasonably well with previously published laboratory bioassay data. SeMNPV killed second and fourth instar S. exigua larvae approximately 12 h faster than did AcMNPV in chrysanthemum, but no difference in speed of action was found for third instar larvae. The relative speed of action of AcMNPV and SeMNPV determined in chrysanthemum and in laboratory bioassays did not correspond for third instar S. exigua larvae; laboratory bioassay data can therefore not simply be extrapolated to the crop level. 相似文献