Parameter Estimation in a PDE Model for the Spatial Spread of Cocoa Black Pod Disease.

In this paper, we develop an epidemiological model with both environmental (primary infection from the environmental spores reservoir) and direct transmission (secondary infection from an infected host to a susceptible pod). This model simulates the spatiotemporal evolution of cocoa black pod disease caused by Phytophthora megakarya. Since reliable parameter estimation is a central issue for modeling realistic biological systems, we used a mechanistic-statistical approach to estimate model parameters from real observations of a specific cocoa plot. In addition, to refine numerical simulations of the pathosystem, data describing the shade intensity all over the plot were exploited and led to increased model predictions accuracy and also highlighted a higher number of infected pods located in areas of the plot with higher shading intensity. Recommendations in terms of promoting cocoa farming in systems with low shading intensity may be evident if these results are confirmed. Our results also highlight the importance of the environmental spore reservoir in black pod disease dynamics.

Using genetic data to estimate diffusion rates in heterogeneous landscapes.

Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

A landscape-scale field survey demonstrates the role of wheat volunteers as a local and diversified source of leaf rust inoculum.

Deploying disease-resistant cultivars is one of the most effective control strategies to manage crop diseases such as wheat leaf rust, caused by Puccinia triticina. After harvest, this biotrophic fungal pathogen can survive on wheat volunteers present at landscape scale and constitute a local source of primary inoculum for the next cropping season. In this study, we characterised the diversity of P. triticina populations surveyed on wheat volunteer seedlings for six consecutive years (2007-2012) at the landscape scale. A total of 642 leaf rust samples classified in 52 virulence profiles (pathotypes) were collected within a fixed 5-km radius. The pathotype composition (identity and abundance) of field-collected populations was analyzed according to the distance between the surveyed wheat plots and to the cultivars of origin of isolates. Our study emphasised the high diversity of P. triticina populations on wheat volunteers at the landscape scale. We observed an impact of cultivar of origin on pathogen population composition. Levels of population diversity differed between cultivars and their deployment in the study area. Our results suggest that wheat volunteers could provide a significant though highly variable contribution to the composition of primary inoculum and subsequent initiation of leaf rust epidemics.

Computing Geographical Networks Generated by Air-Mass Movement.

As air masses move within the troposphere, they transport a multitude of components including gases and particles such as pollen and microorganisms. These movements generate atmospheric highways that connect geographic areas at distant, local, and global scales that particles can ride depending on their aerodynamic properties and their reaction to environmental conditions. In this article we present an approach and an accompanying web application called tropolink for measuring the extent to which distant locations are potentially connected by air-mass movement. This approach is based on the computation of trajectories of air masses with the HYSPLIT atmospheric transport and dispersion model, and on the computation of connection frequencies, called connectivities, in the purpose of building trajectory-based geographical networks. It is illustrated for different spatial and temporal scales with three case studies related to plant epidemiology. The web application that we designed allows the user to easily perform intensive computation and mobilize massive archived gridded meteorological data to build weighted directed networks. The analysis of such networks allowed us for example, to describe the potential of invasion of a migratory pest beyond its actual distribution. Our approach could also be used to compute geographical networks generated by air-mass movement for diverse application domains, for example, to assess long-term risk of spread from persistent or recurrent sources of pollutants, including wildfire smoke.

Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction.

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.

A parsimonious approach for spatial transmission and heterogeneity in the COVID-19 propagation.

Raw data on the number of deaths at a country level generally indicate a spatially variable distribution of COVID-19 incidence. An important issue is whether this pattern is a consequence of environmental heterogeneities, such as the climatic conditions, during the course of the outbreak. Another fundamental issue is to understand the spatial spreading of COVID-19. To address these questions, we consider four candidate epidemiological models with varying complexity in terms of initial conditions, contact rates and non-local transmissions, and we fit them to French mortality data with a mixed probabilistic-ODE approach. Using statistical criteria, we select the model with non-local transmission corresponding to a diffusion on the graph of counties that depends on the geographic proximity, with time-dependent contact rate and spatially constant parameters. This suggests that in a geographically middle size centralized country such as France, once the epidemic is established, the effect of global processes such as restriction policies and sanitary measures overwhelms the effect of local factors. Additionally, this approach reveals the latent epidemiological dynamics including the local level of immunity, and allows us to evaluate the role of non-local interactions on the future spread of the disease.

Spatiotemporal structure of host-pathogen interactions in a metapopulation.

The ecological and evolutionary dynamics of species are influenced by spatiotemporal variation in population size. Unfortunately, we are usually limited in our ability to investigate the numerical dynamics of natural populations across large spatial scales and over long periods of time. Here we combine mechanistic and statistical approaches to reconstruct continuous-time infection dynamics of an obligate fungal pathogen on the basis of discrete-time occurrence data. The pathogen, Podosphaera plantaginis, infects its host plant, Plantago lanceolata, in a metapopulation setting where the presence of the pathogen has been recorded annually for 6 years in approximately 4,000 host populations across an area of 50 km x 70 km in Finland. The dynamics are driven by strong seasonality, with a high extinction rate during winter and epidemic expansion in summer for local pathogen populations. We are able to identify with our model the regions in the study area where overwintering has been most successful. These overwintering sites represent foci that initiate local epidemics during the growing season. There is striking heterogeneity at the regional scale in both the overwintering success of the pathogen and the encounter intensity between the host and the pathogen. Such heterogeneity has profound implications for the coevolutionary dynamics of the interaction.

Mechanical-statistical modeling in ecology: from outbreak detections to pest dynamics.

Knowledge about large-scale and long-term dynamics of (natural) populations is required to assess the efficiency of control strategies, the potential for long-term persistence, and the adaptability to global changes such as habitat fragmentation and global warming. For most natural populations, such as pest populations, large-scale and long-term surveys cannot be carried out at a high resolution. For instance, for population dynamics characterized by irregular abundance explosions, i.e., outbreaks, it is common to report detected outbreaks rather than measuring the population density at every location and time event. Here, we propose a mechanical-statistical model for analyzing such outbreak occurrence data and making inference about population dynamics. This spatio-temporal model contains the main mechanisms of the dynamics and describes the observation process. This construction enables us to account for the discrepancy between the phenomenon scale and the sampling scale. We propose the Bayesian method to estimate model parameters, pest densities and hidden factors, i.e., variables involved in the dynamics but not observed. The model was specified and used to learn about the dynamics of the European pine sawfly (Neodiprion sertifer Geoffr., an insect causing major defoliation of pines in northern Europe) based on Finnish sawfly data covering the years 1961-1990. In this application, a dynamical Beverton-Holt model including a hidden regime variable was incorporated into the model to deal with large variations in the population densities. Our results gave support to the idea that pine sawfly dynamics should be studied as metapopulations with alternative equilibria. The results confirmed the importance of extreme minimum winter temperatures for the occurrence of European pine sawfly outbreaks. The strong positive connection between the ratio of lake area over total area and outbreaks was quantified for the first time.

Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases.

Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host (e.g. individual, household, field). However, modern sequencing techniques can reveal the polymorphic nature of within-host populations of pathogens. Thus, these techniques provide a subsample of the pathogen variants that were present in the host at the sampling time. Such data are expected to give more insight on epidemiological links than a single sequence per host. In general, a mechanistic viewpoint to transmission and micro-evolution has been followed to infer epidemiological links from these data. Here, we investigate an alternative approach grounded on statistical learning. The idea consists of learning the structure of epidemiological links with a pseudo-evolutionary model applied to training data obtained from contact tracing, for example, and using this initial stage to infer links for the whole dataset. Such an approach has the potential to be particularly valuable in the case of a risk of erroneous mechanistic assumptions, it is sufficiently parsimonious to allow the handling of big datasets in the future, and it is versatile enough to be applied to very different contexts from animal, human and plant epidemiology. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.

Time course of the use of chromatic and achromatic facial information for sex categorization.

The most useful facial features for sex categorization are the eyes, the eyebrows, and the mouth. Dupuis-Roy et al. reported a large positive correlation between the use of the mouth region and rapid correct answers [Journal of Vision 9 (2009) 1-8]. Given the chromatic information in this region, they hypothesized that the extraction of chromatic and achromatic cues may have different time courses. Here, we tested this hypothesis directly: 110 participants categorized the sex of 300 face images whose chromatic and achromatic content was partially revealed through time (200 ms) and space using randomly located spatio-temporal Gaussian apertures (i.e. the Bubbles technique). This also allowed us to directly compare, for the first time, the relative importance of chromatic and achromatic facial cues for sex categorization. Results showed that face-sex categorization relies mostly on achromatic (luminance) information concentrated in the eye and eyebrow regions, especially the left eye and eyebrow. Additional analyses indicated that chromatic information located in the mouth/philtrum region was used earlier-peaking as early as 35 ms after stimulus onset-than achromatic information in the eye regions-peaking between 165 and 176 ms after stimulus onset-as was speculated by Dupuis-Roy et al. A non-linear analysis failed to support Yip and Sinha's proposal that processing of chromatic variations can improve subsequent processing of achromatic spatial cues, possibly via surface segmentation [Perception 31 (2002) 995-1003]. Instead, we argue that the brain prioritizes chromatic information to compensate for the sluggishness of chromatic processing in early visual areas, and allow chromatic and achromatic information to reach higher-level visual areas simultaneously.

DNA-PK phosphorylation sites on Oct-1 promote cell survival following DNA damage.

Octamer transcription factor-1 (Oct-1) has recently been shown to function as a stress sensor that promotes cell survival subsequent to DNA damage. Here, we show that the survival signal imparted by Oct-1 following exposure to ionizing radiation (IR) is dependent upon DNA-dependent protein kinase (DNA-PK)-dependent phosphorylation of a cluster of 13 specific ser/thr residues within the N-terminal transcriptional regulatory domain of Oct-1. Although IR treatment did not affect the recruitment of Oct-1 to the histone H2B promoter, the recruitment of RNA polymerase II, TATA-binding protein and histone H4 acetylation were strongly reduced, consistent with a decrease in Oct-1 transcriptional regulatory potential following IR exposure. Ser/Thr-Ala substitution of 13 sites present in Oct-1 transcriptional regulatory domain eliminated Oct-1 phosphorylation subsequent to IR exposure. Further, these substitutions prevented Oct-1 from rescuing the survival of IR-treated Oct-1-/- murine embryonic fibroblasts, providing a direct link between DNA-PK-dependent phosphorylation and the contribution of Oct-1 to cell survival. These results implicate Oct-1 as a primary effector in a DNA-PK-dependent cell survival pathway that is activated by double-stranded DNA breaks.

Accounting for biological variability and sampling scale: a multi-scale approach to building epidemic models.

When one considers the fine-scale spread of an epidemic, one usually knows the sources of biological variability and their qualitative effect on the epidemic process. The force of infection on a susceptible unit depends on the locations and the strengths of the infectious units, and on the environmental and intrinsic factors affecting infectivity and/or susceptibility. The infection probability for the susceptible unit can then be modelled as a function of these factors. Thus, one can build a conceptual model at the fine scale. However, the epidemic is generally observed at a larger scale and one has to build a model adapted to this larger scale. But how can the sources of variation identified at the fine scale be integrated into the model at the larger scale? To answer this question, we present, in the context of plant epidemiology, a multi-scale approach which consists of defining a base model built at the fine scale and upscaling it to match the scale of the sampling and the data. This approach will enable comparing experiments involving different observational processes.

Anisotropy, in density and in distance, of the dispersal of yellow rust of wheat: experiments in large field plots and estimation.

ABSTRACT Long-distance dispersal of spores generally presents anisotropy. This anisotropy can appear in the mean number of spores deposited along a given direction (anisotropy in density) and in the mean distance that a spore travels in a given direction (anisotropy in distance). Specific experiments together with a statistical methodology are proposed to study this effect. The experiments are based on the use of a point source of a traceable inoculum and susceptible trap plots in large resistant field plots. The anisotropy is characterized by two functions: a directional density function and a mean distance function which are related with the anisotropies in density and distance, respectively. A nonparametric approach is developed to estimate these functions and to help in choosing a parametric model. Then, the parametric model is estimated. In two field experiments, migrations up to 175 and 225 m from the source were detected, with approximately 25% of the trap plots infected. Whatever the experiment, the two estimated anisotropies presented different shapes (i.e., the number of spores dispersed in a given direction was not proportional to the mean distance travelled by these spores).

Novel seminal phospholipase A2 is inhibited by the major proteins of bovine seminal plasma.

The activity of a novel phospholipase A2, isolated from bovine seminal plasma, was completely inhibited by low concentrations of the major proteins of bovine seminal plasma (BSP proteins). The inhibition was observed towards micellar as well as liposomal phosphatidylcholine. By solid phase binding assay it was determined that the inhibition involved a reduced accessibility to the lipidic substrate. Since the BSP proteins interact with choline phospholipids and since this interaction can be prevented by low concentrations of free choline, the effect of choline on the inhibition was studied. Choline could only partially relieve, even at high concentrations, the phospholipase A2 inhibition. The reduced accessibility appears to proceed via two distinct interactions: binding to the substrate on one hand and to the enzyme on the other hand. These results indicate that the BSP proteins may act as spermatozoa stabilizing agents by preventing premature lipolysis of the sperm surface.

Bovine seminal platelet-activating factor acetylhydrolase: association properties in seminal plasma and with lipoproteins.

The enzyme responsible for most of the phospholipase A2 (PLA2) activity present in bovine seminal plasma was recently purified to homogeneity. Sequencing revealed that the enzyme is also a platelet-activating factor acetylhydrolase (PAF-AH) of the serum type with kinetic properties generally similar to its serum homologue. In the present work, we have attempted to clarify its physiological function by studying its association properties in seminal plasma. As was observed previously for its PLA2 activity, its PAF-AH activity was also inhibited by the major proteins of bovine seminal plasma (BSP proteins). Sequential dilution experiments as well as centrifuging semen on Percoll did not reveal detectable association of PAF-AH with spermatozoa. Neither did the enzyme interact with lipid particles reported to be present in bovine seminal plasma. The purified PAF-AH, however, did display lipoprotein association properties in vitro similar to those demonstrated by the serum enzyme in vivo. At pH 7.4, it could associate with both low density lipoproteins and very low density lipoproteins but not with high density lipoproteins. Overall the data presented here indicate that the enzyme is strongly inactivated as a PAF-AH in seminal plasma and that it does not associate with lipid particles or spermatozoa.

Single-step isolation of bovine seminal platelet-activating factor acetylhydrolase.

Bovine seminal platelet-activating factor acetylhydrolase was isolated to >90% purity in a single step using a butyl sepharose column. The procedure involves the elution of the activity by use of an ethanol gradient. Protein binds readily to the resin in the absence of high ionic strength and elutes as a peak centered at 30% ethanol. Approximately 2 mg (by Bradford; 5 mg by weight) of the enzyme can thus be easily obtained from 9 ml of seminal plasma. The specific activity of the purified protein was 22 micromol/minute/mg. About 10% of the loaded activity systematically passed unadsorbed through the column, even after repassing. Most of this activity, however, was attributed to the same or a very similar enzyme that cross-reacts with polyclonal antibodies directed against the highly purified platelet-activating factor acetylhydrolase. The enzyme was acid-labile but very resistant to freezing and lyophilization. This purification procedure should constitute a valuable asset to investigators interested in platelet-activating factor and platelet-activating factor acetylhydrolase roles in reproductive biology.

Activation of PARP-1 in response to bleomycin depends on the Ku antigen and protein phosphatase 5.

Poly (ADP-ribose) polymerase-1 (PARP-1) has an important role in the cellular response to a broad spectrum of DNA lesions. PARP-1 is strongly activated in response to double-stranded DNA breaks (DSBs), yet its contribution to the DSB response is poorly understood. Here we used bleomycin, a radiomimetic that generates DSBs with high specificity to focus on the response of PARP-1 to DSBs. We report that the induction of PARP-1 activity by bleomycin depends on the Ku antigen, a nonhomologous-DNA-End-Joining factor and protein phosphatase 5 (PP5). PARP-1 activation in response to bleomycin was reduced over 10-fold in Ku-deficient cells, whereas its activation in response to U.V. was unaffected. PARP-1 activation was rescued by reexpression of Ku, but was refractory to manipulation of DNA-dependent protein kinase or ATM. Similarly, PARP-1 activation subsequent to bleomycin was reduced 2-fold on ablation of PP5 and was increased 5-fold when PP5 was overexpressed. PP5 seemed to act directly on PARP-1, as its basal phosphorylation was reduced on overexpression of PP5, and PP5 dephosphorylated PARP-1 in vitro. These results highlight the functional importance of Ku antigen and PP5 for PARP-1 activity subsequent to DSBs.

Phospholipase A2 from bovine seminal plasma is a platelet-activating factor acetylhydrolase.

The major phospholipase A2 activity from bovine seminal plasma was recently purified [Soubeyrand, Khadir, Brindle and Manjunath (1997) J. Biol. Chem. 272, 222-227]. We here show that the 60 kDa enzyme is in fact a platelet-activating factor acetylhydrolase (PAF-AH). Sequences of the N-terminus as well as of internal fragments showed 100% identity with the cDNA-deduced sequences of bovine plasma PAF-AH. The enzyme has kinetic properties similar to those of the human serum PAF-AH. Although capable of hydrolysing long-chained phosphatidylcholine, it displayed a highly preferential activity towards PAF. The enzyme activity towards phosphatidylcholine, but not PAF, was Ca2+-dependent. Biochemical characterization revealed that the enzyme is extensively N-glycosylated and that it exists predominantly as a dimer in solution. Western blot analysis revealed that the enzyme is highly heterogeneous in charge, with a maximal distribution at an isoelectric point of approx. 5.7. The enzyme was expressed exclusively in the seminal vesicles and the ampulla. No association of the enzyme with either epididymal or ejaculated spermatozoa could be detected.

Major proteins of bovine seminal plasma modulate sperm capacitation by high-density lipoprotein.

Bovine seminal plasma (BSP) contains four similar proteins secreted by the seminal vesicles, designated BSP-A1, -A2, -A3, and -30 kDa. These proteins bind to choline phospholipids on the surface of the sperm after ejaculation. These BSP proteins also interact with heparin, apolipoprotein A-I (apoA-I) and apoA-I associated with high-density lipoprotein (HDL). The HDL and heparin present in the female reproductive tract have been implicated in sperm capacitation and the acrosome reaction (AR). This study was undertaken to determine whether or not these BSP proteins and HDL could modulate the capacitation of sperm, and to determine the combined effect of HDL and heparin on capacitation. Washed bovine epididymal sperm were preincubated in buffer containing BSP proteins, washed, and incubated with lipoproteins (HDL, and low- and very low-density lipoproteins) or liposomes with or without apoA-I in the presence or absence of heparin. The percentage of capacitated sperm was evaluated after the AR was induced with lysophosphatidylcholine. HDL alone (160 microg/ml) after an 8-h incubation stimulated the AR of epididymal sperm. The percentage of HDL-enhanced AR further increased when sperm were preincubated with BSP proteins. ApoA-I-liposomes stimulated the AR more rapidly (5 h, 160 microg/ml) than HDL. When sperm were preincubated with BSP proteins, the percentage of apoA-I-enhanced AR further increased. In contrast, when liposomes without apoA-I or when low- or very low-density lipoproteins or lipoprotein-depleted serum was used, no significant increase in the AR was detected with or without BSP proteins. When heparin and HDL or apoA-I-liposomes were used together, their combined effects on the AR were not additive. These results indicate that BSP proteins modulate the process of capacitation induced by heparin, HDL, and apoA-I-liposomes.

Major proteins of bovine seminal plasma inhibit phospholipase A2.

We have recently shown that the major proteins of bovine seminal plasma, namely BSP-A1, BSP-A2, BSP-A3 and BSP-30-kDa (collectively called BSP proteins) bind to spermatozoa and that the binding sites on the plasma membrane of spermatozoa are choline phospholipids. In view of the fact that these phospholipids are substrates for phospholipase A2 (PLA2), a key enzyme in sperm capacitation and the acrosome reaction, the effect of BSP proteins on this enzyme activity was investigated. Since these BSP proteins are ubiquitous, the effect on pig pancreatic PLA2 was also studied. In contrast with control proteins, when preincubated with phosphatidylcholine as substrate, all BSP proteins inhibited both pancreatic and sperm PLA2 activity in a dose-dependent manner and in the presence of 1-6 microM BSP protein the enzyme activity was completely abolished. When phosphatidylethanolamine was used as substrate, only pancreatic PLA2 was inhibited. On the other hand, when the BSP proteins were preincubated with the enzyme followed by addition of substrate, a biphasic effect was observed; there was stimulation of enzyme activity below 1.3 microM BSP followed by an inhibition above this concentration. The inhibitory activity was trypsin-sensitive but heat-resistant. The effect of co-incubation of heparin, which is implicated in sperm capacitation and which also interacts with BSP proteins, was studied. Heparin (10 microM) had no effect on the PLA2 inhibitory activity exhibited by all BSP proteins. The PLA2 inhibitory effect exhibited by BSP proteins was abolished with excess substrate. The BSP proteins were adsorbed on PLA2-agarose and could be affinity cross-linked to the enzyme, indicating a direct interaction of enzyme with the inhibitor. These results suggest that these BSP proteins modulate PLA2 activity and therefore, phospholipid metabolism.