The role of initial inoculum on epidemic dynamics

Transient dynamics are important in many epidemics in agricultural and ecological systems that are prone to regular disturbance, cyclical and random perturbations. Here, using a simple host-pathogen model for a sessile host and a pathogen that can move by diffusion and advection, we use a range of mathematical techniques to examine the effect of initial spatial distribution of inoculum of the pathogen on the transient dynamics of the epidemic. We consider an isolated patch and a group of patches with different boundary conditions. We first determine bounds on the host population for the full model, then non-dimensionalizing the model allows us to obtain approximate solutions for the system. We identify two biologically intuitive groups of parameters to analyse transient behaviour using perturbation techniques. The first parameter group is a measure of the relative strength of initial primary to secondary infection. The second group is derived from the ratio of host removal rate (via infection) to pathogen removal rate (by decay and natural mortality) and measures the infectivity of initial inoculum on the system. By restricting the model to mimic primary infection only (in which all infections arise from initial inoculum), we obtain exact solutions and demonstrate how these depend on initial conditions, boundary conditions and model parameters. Finally, we suggest that the analyses on the balance of primary and secondary infection provide the epidemiologist with some simple rules to predict the transient behaviours.     

Analysis of ellagitannins and conjugates of ellagic acid and quercetin in raspberry fruits by LC-MSn

The use of gradient reversed phase HPLC with diode array and MS(n) detection for the analysis of ellagitannins, ellagic acid conjugates and quercetin conjugates in raspberries (Rubus idaeus L.) is described. MS(n) is a particularly powerful tool for the analysis of trace levels of natural products in impure extracts as interpretation of fragmentation patterns, coupled in some instances with knowledge of HPLC retention properties, can facilitate the partial identification of components when reference compounds are unavailable.     

Effect of environmental conditions and inoculum density on infection of guava fruits by Colletotrichum glososporioides

The influence of environmental factors (temperature and humidity), inoculum density on infection by Colletotrichum glososporioides and development of anthracnose lesions were determined on uninjured, sand-injured and punctured fruits. The optical temperature for severe infection was 30 °C, whereas the disease incidence was less at 20 and 35 °C. Inoculated guavas that received 1–60 h of continuous free moisture developed lesions, but the disease was minimal (0–7%) after 1–6 h free moisture. Infection rates of uninjured, sand-injured and punctured fruits receiving 60 h of free moisture were 34, 70 and 100%, respectively. Disease incidence increased as inoculum density increased from 101 to 106 conidia/ml. In field conditions, the development of anthracnose lesions was greater on punctured guavas than on uninjured or sand-injured ones, in both rainy and winter seasons. In general, the number of lesions was highest in sand-injured fruits, followed by punctured and uninjured fruits. In rainy season the number of lesions on injured and uninjured fruits was greater than similarly treated guavas in winter. This revised version was published online in June 2006 with corrections to the Cover Date.     

The effect of inoculating flowers and developing fruits with Botrytis cinerea on post-harvest grey mould of red raspberry

Raspberry flowers were inoculated in the glasshouse and field with dry conidia of Botrytis cinerea and the fruits derived from them subjected to post-harvest rot tests at c. 20°C and high humidity. Apparently healthy fully-ripe picked fruits derived from inoculated flowers developed grey mould faster than those from non-inoculated flowers in all tests. In the glasshouse experiments, fruits from inoculated tightly closed flower buds rotted more slowly than those from inoculated open flowers or those at later developmental stages. Fruits from inoculated whole flowers rotted more rapidly than those from emasculated flowers; the addition of pollen to emasculated flowers had little effect on post-harvest grey mould. In the dry summer of 1984 no fruits in the field from inoculated whole flowers rotted before ripening, but in the wet season of 1985 pre-harvest grey mould was common and the surviving healthy fruits rotted in c. 1 day after picking. Only minor differences were detected in host susceptibility to post-harvest grey mould in both glasshouse and field tests, the ranking of genotypes varied depending on whether or not flowers had been inoculated. The susceptibility of pistils of 40 Rubus genotypes to infection was examined 7 and 28 days after inoculation of stigmas with dry conidia. Conidia germinated on the stigmas and produced hyphae which grew through transmitting tissues of the styles to infect carpels symptomlessly in 17 red raspberries, one blackberry, two Rubus spp. and one hybrid. No germination occurred on stigmas of cv. Carnival and New York Selection 817.     

Investigating water and framework dynamics in pillared MOFs

In this work we highlight the use of molecular simulation to study the behaviour of water inside isostructural Zn-DMOF structures. Among the Zn-DMOF structures, the parent DMOF, and the DMOF-DM and DMOF-TF variants are known to be less stable than the DMOF-A and DMOF-TM structures in the presence of water. We apply tools such as radial distribution functions, rotational auto-correlation functions and the visualisation of adsorbate density distributions to investigate the differences in water behaviour within these structures. We also study properties that are inherent to the frameworks themselves such as thermal expansion and ligand flexibility. Our results indicate that water is only able to get 0.5 Å closer to the metal hydrolysis site in the water unstable structures than in the more water stable structures. The results can be somewhat sensitive to the details of the modelling of the electrostatic potential energy surface and, for dynamical properties, modelling of framework flexibility.     

Genetic control of the reactions of raspberry to black raspberry necrosis, raspberry leaf mottle and raspberry leaf spot viruses

Black raspberry necrosis virus (BRNV) induces a severe apical necrosis in black raspberry (Rubus occidentalis) but fails to induce diagnostic symptoms in red raspberry. However, BRNV infection of F₁, F₂ and F₃ hybrids from the cross black raspberry × red raspberry induced mosaic symptoms of varying intensity but no typical apical necrosis. In a survey of 28 red raspberry cultivars, a few developed severe angular chlorotic leaf spots when infected with raspberry leaf mottle virus and a few others did so when infected with raspberry leaf spot virus. These reactions were determined by single dominant genes designated Lm and Ls respectively. The value of the different host reactions for controlling the effects and spread of these viruses is discussed.     

The role as inoculum sources of Xanthomonas citri pv. citri surviving on the infected Satsuma mandarin fruits

Importing citrus fruits infected by Asiatic citrus canker caused by Xanthomonas citri pv. citri (Xcc) can act as an inoculum source for the disease epidemic in citrus canker-free countries. In this study, the pathogenicity of the causal agent of Asiatic citrus canker surviving on infected Satsuma mandarin fruits was evaluated. The washing solution of infected Satsuma mandarin fruits did not cause lesion formation on the citrus leaves. However, a typical citrus canker lesion was formed on the leaves after inoculation with higher concentrations of the inoculum from the washing solution (washing solution II). It indicated that the pathogenicity of the citrus canker surviving on the symptomatic Satsuma mandarin fruits was not changed. Scanning electron microscopic observation showed that the numbers of bacterial cells on the leaves of Satsuma mandarin which inoculated with the washing solution directly (washing solution I) was less compared to those of leaves inoculated with the washing solution II. This result spports that the pathogenicity of Xcc surviving on Satsuma mandarin fruits may not be changed but that the sucessful infection of citrus caker may depend on the concentration of the inoculum.     

Investigating the size and dynamics of voltage-gated sodium channel fenestrations

Eukaryotic voltage-gated sodium channels (VGSCs) are essential for the initiation and propagation of action potentials in electrically excitable cells, and are important pharmaceutical targets for the treatment of neurological disorders such as epilepsy, cardiac arrhythmias, and chronic pain. Evidence suggests that small, hydrophobic, VGSC-blocking drugs can gain access to binding residues within the central cavity of these channels by passing through lateral, lipid-filled “fenestrations” which run between the exterior of the protein and its central pore. Here, we use molecular dynamics simulations to investigate how the size and shape of fenestrations change over time in several bacterial VGSC models and a homology model of Nav1.4. We show that over the course of the simulations, the size of the fenestrations is primarily influenced by rapid protein motions, such as amino acid side-chain rotation, and highlight that differences between fenestration bottleneck-contributing residues are the primary cause of variations in fenestration size between the 6 bacterial models. In the eukaryotic channel model, 2 fenestrations are wide, but 2 are narrow due to differences in the amino acid sequence in the 4 domains. Lipid molecules are found to influence the size of the fenestrations by protruding acyl chains into the fenestrations and displacing amino acid side-chains. Together, the results suggest that fenestrations provide viable pathways for small, flexible, hydrophobic drugs.     

Investigating the size and dynamics of voltage-gated sodium channel fenestrations: A molecular dynamics study

Eukaryotic voltage-gated sodium channels (VGSCs) are essential for the initiation and propagation of action potentials in electrically excitable cells, and are important pharmaceutical targets for the treatment of neurological disorders such as epilepsy, cardiac arrhythmias, and chronic pain. Evidence suggests that small, hydrophobic, VGSC-blocking drugs can gain access to binding residues within the central cavity of these channels by passing through lateral, lipid-filled “fenestrations” which run between the exterior of the protein and its central pore. Here, we use molecular dynamics simulations to investigate how the size and shape of fenestrations change over time in several bacterial VGSC models and a homology model of Nav1.4. We show that over the course of the simulations, the size of the fenestrations is primarily influenced by rapid protein motions, such as amino acid side-chain rotation, and highlight that differences between fenestration bottleneck-contributing residues are the primary cause of variations in fenestration size between the 6 bacterial models. In the eukaryotic channel model, 2 fenestrations are wide, but 2 are narrow due to differences in the amino acid sequence in the 4 domains. Lipid molecules are found to influence the size of the fenestrations by protruding acyl chains into the fenestrations and displacing amino acid side-chains. Together, the results suggest that fenestrations provide viable pathways for small, flexible, hydrophobic drugs.     

Investigating membrane protein dynamics in living cells.

Live cell imaging is a powerful tool for understanding the function and regulation of membrane proteins. In this review, we briefly discuss 4 fluorescence-microscopy-based techniques for studying the transport dynamics of membrane proteins: fluorescence-correlation spectroscopy, image-correlation spectroscopy, fluorescence recovery after photobleaching, and single-particle and (or) molecule tracking. The advantages and limitations of each approach are illustrated using recent studies of an ion channel and cell adhesion molecules.     

Investigating protein dynamics in collective coordinate space.

Currently, collective coordinates are commonly employed in order to examine protein dynamics. In recent studies, they have been successfully applied to finding functionally relevant motions, to investigating the physical nature of protein dynamics, to sampling of the conformational space and to the analysis of experimental data. Collective coordinates also have other possible applications.     

Investigating the effects of vacancies on self-diffusion in silicon clusters using classical molecular dynamics

Due to recent advances in the field of microelectronics, the growth in microelectronics applications, and the exponentially increasing demand for microelectronic devices in the power sector, it is important to study the behavior of silicon at the nanoscale, given that nanoclusters of silicon could be used to design a new kind of lithium-ion batteries with strongly enhanced performance. Here, molecular dynamics was employed to calculate the self-diffusion coefficients of silicon clusters at room temperature and at a temperature approaching the melting point of silicon, complementing experimental efforts in this field. Silicon clusters of the same spherical geometry and size but with different vacancy fractions were studied using molecular dynamics using the Tersoff potential in order to estimate phase changes and self-diffusion coefficients. At 300 K, the self-diffusion coefficient was found to vary non-monotonically: the self-diffusion coefficient at a vacancy fraction of 7.5% is half than the vacancy at a fraction of 0%, while the self-diffusion coefficient at a vacancy fraction of 20% is two orders of magnitude larger than that at a vacancy fraction of 0%. However, there is only a marginal monotonic increase in the self-diffusion coefficient values with vacancy fraction at 2000 K. The results of this investigation of vacancy-mediated self-diffusion could aid attempts to improve diffusion control, which is crucial to nanocluster applications in various devices, and the results also provide insight into how the temperature, energy, pressure, and phase changes of the silicon clusters depend on vacancy fraction. This may ultimately allow the design and selection of materials for thermoelectric and optoelectronic devices and thermal transducers to be optimized. Our results also indicated that the findings we obtained for the clusters are independent of the particular random vacancy distribution considered and the heating rate applied to the clusters.

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Graphical Abstract Silicon nanoparticles (SNP) are among the best options to choose from for the design of devices for renewable energies; SNP based material performance can be effectively tailored by controling the vacancy, temperature and other properties of the SNP.

     

Temperature mediates vector transmission efficiency: inoculum supply and plant infection dynamics

Climate, particularly environmental temperature, frequently plays an important role in disease epidemiology. This study investigated the role of environmental temperature on transmission of the generalist plant pathogen Xylella fastidiosa by its leafhopper vectors. In this system temperature is known to influence both vector performance and feeding rate, yet the implications for pathogen transmission have not been documented. Experiments were conducted over a range of temperatures to document effects on transmission efficiency of the California native Graphocephala atropunctata (blue–green sharpshooter) and the invasive Homalodisca vitripennis (glassy-winged sharpshooter). Inoculation efficiency of H. vitripennis was positively related to temperature. Graphocephala atropunctata mortality and transmission responded non-linearly to temperature, with the highest rates of both at the highest temperature. The experiment also evaluated whether differences in inoculum supply contributed to plant infection level using quantitative PCR. Although total X. fastidiosa population within G. atropunctata was not related to plant infection, the number of infectious vectors was a strong predictor of plant infection level–suggesting that the number of inoculation events is important in the development of systemic infection of X. fastidiosa in grapevines. These results, along with existing evidence from the literature, point to wide-ranging impacts of climate on the epidemiology of X. fastidiosa diseases.     

Zika virus dynamics: Effects of inoculum dose,the innate immune response and viral interference

Experimental Zika virus infection in non-human primates results in acute viral load dynamics that can be well-described by mathematical models. The inoculum dose that would be received in a natural infection setting is likely lower than the experimental infections and how this difference affects the viral dynamics and immune response is unclear. Here we study a dataset of experimental infection of non-human primates with a range of doses of Zika virus. We develop new models of infection incorporating both an innate immune response and viral interference with that response. We find that such a model explains the data better than models with no interaction between virus and the immune response. We also find that larger inoculum doses lead to faster dynamics of infection, but approximately the same total amount of viral production.     

Colonization by Cladosporium spp. of painted metal surfaces associated with heating and air conditioning systems

Cladosporium cladosporioides and C. hebarum colonized painted metal surfaces of covering panels and register vents of heating, air conditioning and ventilation systems. Hyphae penetrated the paint film and developed characteristic conidiophores and conidia. The colonies were tightly appressed to the metal surface and conidia were not readily detectable via standard air sampling procedures.