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.

     

Explaining urban governance in the midst of political transformation: The city of Macao

This paper takes a close look at the urban governance and political culture of Macao, the world largest casino city. Macao has experienced spectacular economic growth since gaming liberalisation in 2002 and China's Free Individual Travel scheme launched in 2003. However, the booming gaming sector has crowded out other sectors of Macao. It has not only made the city's economy mono‐structured and consequently extremely vulnerable to external shocks and fluctuations but also induced serious social divisions and political controversies within the local community. By tracing the root cause of the ongoing dilemma and crisis in the mode of governance, the dynamic relationships between formal and informal institutions, consensus politics and the social group culture are intensively discussed in a historical context. In fact, the sustainable development of the former Portuguese colony has largely been hindered by its residents' passive attitudes toward political communication, non‐transparent urban governance, the absence of a middle class and the dominance of pro‐establishment social groups.     

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.     

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.     

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.     

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.     

Seed Potato Quality Improvement through Positive Selection by Smallholder Farmers in Kenya

In Kenya, seed potato quality is often a major yield constraint in potato production as smallholder farmers use farm-saved seed without proper management of seed-borne pests and diseases. Farm-saved seed is therefore often highly degenerated. We carried out on-farm research to assess whether farmer-managed positive seed selection could improve yield. Positive selection gave an average yield increase in farmer-managed trials of 34%, corresponding to a 284-€ increase in profit per hectare at an additional production cost of only 6 €/ha. Positive selection can be an important alternative and complementary technology to regular seed replacement, especially in the context of imperfect rural economies characterized by high risks of production and insecure markets. It does not require cash investments and is thus accessible for all potato producers. It can also be applied where access to high-quality seed is not guaranteed. The technology is also suitable for landraces and not recognized cultivars that cannot be multiplied formally. Finally, the technology fits seamlessly within the seed systems of Sub-Saharan Africa, which are dominated by self-supply and neighbour supply of seed potatoes.     

Impacts of increased fire frequency and aridity on eucalypt forest structure,biomass and composition in southwest Australia

Water stress and fire disturbance can directly impact stand structure, biomass and composition by causing mortality and influencing competitive interactions among trees. However, open eucalypt forests of southwest Australia are highly resilient to fire and drought and may respond differently to increased fire frequency and aridity than forests dominated by non-eucalypt species. We measured the variation in stem density, basal area, stand biomass, sapwood area, leaf area and litterfall across 16 mixed jarrah (Eucalyptus marginata) and marri (Corymbia calophylla) forest stands along an aridity gradient in southwest Australia that had variable fire histories. Fire frequency was defined as the total number of fires over a ∼30-year period and aridity as the ratio of potential evapotranspiration to annual precipitation. Total stand biomass and sapwood area were predicted from diameter at breast height of individual jarrah and marri trees using allometric equations. Leaf area was estimated using digital cover photography. More arid and frequently burnt stands had higher stem density, especially of smaller trees, which were mainly jarrah. Overall, both standing biomass and leaf area decreased at more arid sites, while sapwood area was largely unaffected by aridity, suggesting that these stands respond to increased water limitation by decreasing their leaf area relative to their sapwood area. Biomass of marri was reduced at more arid and, to a lesser extent, at more frequently burnt stands. However, total stand biomass (jarrah and marri) and leaf area index did not vary with fire frequency, suggesting that less marri biomass (due to slower growth rates, higher mortality or less recruitment) was compensated by an increase in the density of jarrah trees (regeneration). We conclude that increased fire and drought shift tree species composition towards more fire-resistant species and result in denser stands of smaller trees. In contrast, total stand biomass declines with increasing aridity, but has no association with fire frequency.