A novel epidemiological model to better understand and predict the observed seasonal spread of Pestivirus in Pyrenean chamois populations

Seasonal variations in individual contacts give rise to a complex interplay between host demography and pathogen transmission. This is particularly true for wild populations, which highly depend on their natural habitat. These seasonal cycles induce variations in pathogen transmission. The seasonality of these biological processes should therefore be considered to better represent and predict pathogen spread. In this study, we sought to better understand how the seasonality of both the demography and social contacts of a mountain ungulate population impacts the spread of a pestivirus within, and the dynamics of, this population. We propose a mathematical model to represent this complex biological system. The pestivirus can be transmitted both horizontally through direct contact and vertically in utero. Vertical transmission leads to abortion or to the birth of persistently infected animals with a short life expectancy. Horizontal transmission involves a complex dynamics because of seasonal variations in contact among sexes and age classes. We performed a sensitivity analysis that identified transmission rates and disease-related mortality as key parameters. We then used data from a long-term demographic and epidemiological survey of the studied population to estimate these mostly unknown epidemiological parameters. Our model adequately represents the system dynamics, observations and model predictions showing similar seasonal patterns. We show that the virus has a significant impact on population dynamics, and that persistently infected animals play a major role in the epidemic dynamics. Modeling the seasonal dynamics allowed us to obtain realistic prediction and to identify key parameters of transmission.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-015-0218-8) contains supplementary material, which is available to authorized users.     

Automated detection and tracking of marine mammals: A novel sonar tool for monitoring effects of marine industry

1. Many marine industries may pose acute risks to marine wildlife. For example, tidal turbines have the potential to injure or kill marine mammals through collisions with turbine blades. However, the quantification of collision risk is currently limited by a lack of suitable technologies to collect long‐term data on marine mammal behaviour around tidal turbines.
2. Sonar provides a potential means of tracking marine mammals around tidal turbines. However, its effectiveness for long‐term data collection is hindered by the large data volumes and the need for manual validation of detections. Therefore, the aim here was to develop and test automated classification algorithms for marine mammals in sonar data.
3. Data on the movements of harbour seals were collected in a tidally energetic environment using a high‐frequency multibeam sonar on a custom designed seabed‐mounted platform. The study area was monitored by observers to provide visual validation of seals and other targets detected by the sonar.
4. Sixty‐five confirmed seals and 96 other targets were detected by the sonar. Movement and shape parameters associated with each target were extracted and used to develop a series of classification algorithms. Kernel support vector machines were used to classify targets (seal vs. nonseal) and cross‐validation analyses were carried out to quantify classifier efficiency.
5. The best‐fit kernel support vector machine correctly classified all the confirmed seals but misclassified a small percentage of non‐seal targets (~8%) as seals. Shape and non‐spectral movement parameters were considered to be the most important in achieving successful classification.
6. Results indicate that sonar is an effective method for detecting and tracking seals in tidal environments, and the automated classification approach developed here provides a key tool that could be applied to collecting long‐term behavioural data around anthropogenic activities such as tidal turbines.

     

Development of primers and a procedure for specific identification of the diatom <Emphasis Type="Italic">Thalassiosira weissflogii</Emphasis>

A recent study showed Thalassiosira weissflogii to be a diatom containing suitable nutrition for larviculture of the black tiger shrimp, Penaeus monodon. Accurate and practical identification of this diatom species is therefore important for commercial hatcheries. The purpose of this study was to establish a DNA-based method of identification to supplement morphological examination, avoiding confusion with other Thalassiosira sp. Primers, 18SF/28SR1, specific for ribosomal DNA genes (3′-end of 18S rDNA through 5′-end of 28S rDNA, covering two internal transcribed spacers), were employed as a first-step polymerase chain reaction, followed by a second nested amplification using specifically designed primers, ITS1-F-D/ITS1-R-D. The nested-PCR result revealed specificity in the detection, distinguishing T. weissflogii from T. pseudonana, Cyclotella meneghiniana, and Chaetoceros sp., and the PCR fragment of the amplified region had a sequence that was 99% identical to the T. weissflogii sequence held by GenBank.     

Enhancement of survival and metamorphosis rates of <Emphasis Type="Italic">Penaeus monodon</Emphasis> larvae by feeding with the diatom <Emphasis Type="Italic">Thalassiosira weissflogii</Emphasis>

The purpose of this study was to compare the performance of two species of diatoms, Thalassiosira weissflogii and Chaetoceros gracilis, in the larviculture of the black tiger shrimp Penaeus monodon. Shrimp larvae were fed with either C. gracilis, T. weissflogii, or a combination of the two species of diatoms. The larvae fed solely with T. weissflogii or a combination of the two types of diatom had significantly higher survival rates and faster metamorphosis than those fed solely with C. gracilis. The numbers of diatom cells consumed by larvae during 3-h periods were determined, revealing that larvae consumed significantly higher numbers of C. gracilis than T. weissflogii. However, when the protein, total fatty acid, and polyunsaturated fatty acid content of the two species of diatom are compared, significantly higher amounts of each are found in T. weissflogii. Converting the number of diatom cells consumed into equivalent protein, total fatty acid, eicosopentaenoic acid, and decosahexaenoic acid reveals that larvae fed with T. weissflogii received significantly higher amounts of all the nutrients, compared to those consuming C. gracilis. The results showed an advantage of feeding T. weissflogii to C. gracilis in enhancing survival and metamorphosis in P. monodon larvae.     

Effect of apple particle state on the release of volatile compounds in a new artificial mouth device

Varying the crushing parameters in a model mouth apparatus gave different crushed apple samples, which were compared to apples crushed in the human mouth by six people. An image analysis method was developed to measure the similarity between apple particles after crushing in the artificial mouth and in the human mouth. Thus, experimental conditions were determined that produced fruit in a state closest to that obtained after mastication in a human mouth. The influence of these different conditions on the quantity of released volatile compounds was then studied.     

Phosphatase activity, microbial phosphorus, and fine root growth in forest soils in the Sierra de Gata, western central Spain

Acid phosphatase activity (APA), labile P fractions and fine root growth were studied in an oak (Quercus pyrenaica Willd.) forest in the Sierra de Gata, in western central Spain. Soils in the region are acid and rich in organic matter, with low levels of extractable inorganic P but with a high proportion of organic P. In such soils, the activity of phosphatase enzymes is likely to be important for the control of P mineralization and P cycling and, consequently, can affect the availability of P for plant uptake. The biomass of fine roots was about 25-fold that of leaf litter, demonstrating a high allocation of C resources to the root system in order to compensate for a low availability of soil nutrients. The study compared plots fertilized with triple superphosphate (100 kg P ha^-1) to control (unfertilized) plots. Fertilizer application had no significant effect on APA and fine root density; however, there were significant differences in available and microbial P. Spatial and seasonal variations in the APA were related to plant root density and biotic demand. Seasonal differences in the APA may also be the consequence of changes in the amount of hydrolysable organic substrates at different times of the year.     

A new approach for modelling vertical stress distribution at the soil/tyre interface to predict the compaction of cultivated soils by using the PLAXIS code

Soil compaction by agricultural machines can have adverse effects on crop production and the environment. Different models based on the Finite Element Method have been proposed to calculate soil compaction intensity as a function of vehicle and soil properties. One problem when modelling soil compaction due to traffic is the estimation of vertical stress distribution at the soil surface, as the vertical stress is inhomogeneous (non-uniform) and depends on soil and tyre properties. However, uniform stress distribution at the soil/tyre interface is used to predict the compaction of cultivated soils in most FEM compaction models. We propose a new approach to numerically model vertical stress distribution perpendicular to the driving direction at the soil/tyre interface, employing the FEM models of PLAXIS code. The approach consists of a beam (characterised by its geometric dimensions and flexural rigidity) introduced at the soil surface and loaded with a uniform stress with the aim to simulate the action of a wheel at the soil surface. Different shapes of stress distribution are then obtained numerically at the soil surface by varying the flexural rigidity of the beam and the mechanical parameters of the soil. PLAXIS simulations show that the soil type (soil texture) modifies the shape of the stress distribution at the edges of the contact interface: a parabolic form is obtained for sand, whereas a U-shaped is obtained for clay. The flexural rigidity of the beam changes the shape of distribution which varies from a homogenous (uniform) to an inhomogeneous distribution (parabolic or U-shaped distribution). These results agree with the measurements of stress distributions for different soils in the literature. We compared simulations of bulk density using PLAXIS to measurement data from compaction tests on a loamy soil. The results show that simulations are improved when using a U-shaped vertical stress distribution which replaces a homogenous one. Therefore, the use of a beam (cylinder) with various flexural rigidities at the soil surface can be used to generate the appropriate distribution of vertical stress for soil compaction modelling during traffic.     

Photosynthesis of a scots pine shoot: simulation of the irradiance distribution and photosynthesis of a shoot in different radiation fields

Using a model of shoot geometry the distribution of irradiance at the needle surface area of a shoot in different radiation conditions is simulated and shoot photosynthesis calculated. It is shown that the distribution of irradiance is very sensitive to radiation field geometry, affecting the efficiency of the utilization of radiant energy in photosynthesis. As a result, the photosynthetic response of a shoot in natural conditions is, for instance, highly dependent on the proportions of direct and diffuse solar radiation, being higher the greater is the proportion of diffuse radiation.     

不同灌水方式下基于水面蒸发量的夏玉米灌溉试验研究

为了探索依据水面蒸发量确定灌溉定额的可行性,在防雨棚下测坑中进行了夏玉米灌溉试验。结果表明,从总耗水量看,畦灌略高于沟灌,而沟灌又略高于滴灌,但差别不是很大。畦灌条件下植株发育快,滴灌次之,沟灌最慢。畦灌和滴灌下产量均以中等灌溉定额处理最高,而沟灌下产量以最大灌溉定额处理最高。总体上,滴灌条件下水分利用效率高于其他2种灌溉方式。干旱条件下,畦灌下以E601蒸发皿蒸发量(PE)作为夏玉米灌溉定额,每次灌水60mm;滴灌下以2/3PE作为灌溉定额为宜,灌水定额为20mm。