A case study of capture-recapture methodology using scrapie surveillance data in Great Britain

We applied capture–recapture methodology (CRC) to data from three surveillance sources (statutory notification, abattoir survey (AS) and fallen stock (FS) survey) to estimate the number of holdings infected with scrapie in Great Britain and to assess the sensitivity of the surveillance network. Between January 1, 2002 and March 31, 2003, 144 holdings were identified by the three sources. Using CRC modelling techniques, we estimated a minimum lower bound for the total number of holdings infected as 642. A biologically plausible positive dependence between the statutory reporting and the fallen stock survey was found statistically significant. The sensitivity of the three sources combined was very low. The integration of the three overlapping sources provided a better understanding of the interactions within the surveillance network. However, the scarcity of the data and reduced overlapping among sources only allowed for very cautious inferences to be drawn about the true proportion of scrapie affected holdings in the national population. Future surveys and surveillance activities should be planned such that the resulting data can be used more effectively as part of CRC modelling approaches.     

Seroprevalences for ovine enzootic abortion in Switzerland

Our aim was to assess the seroprevalence of Chlamydophila (Cd) abortus (Chlamydia psittaci serotype 1), denoted ovine enzootic abortion (OEA), in the Swiss sheep population. A competitive enzyme-linked immunosorbent assay (cELISA) was adapted for the investigation of pooled serum samples (pool approach) and receiver-operator characteristic (ROC) analysis was applied to define the cut-off of the pool approach. At a cut-off value of 30% inhibition, the flock-level pooled sensitivity and specificity were 92.9% and 97.6% when compared to classifying the flock based on individual-animal samples.

Subsequently, sera from 775 randomly selected flocks out of 11 cantons of Switzerland were investigated using the pool approach. The cantons included in the study represented 72% of the Swiss sheep flocks and 76% of Swiss sheep population. Antibodies against Cd. abortus were found in almost 19% (144) of the 775 examined sheep flocks. Test prevalences were adjusted for the imperfect test characteristics using the Rogan–Gladen estimator and Bayesian inference. Seroprevalence was highest (43%) in the canton Graubünden. In the remaining 10 cantons the seroprevalence ranged from 2 to 29%. The cELISA in combination with testing pooled sera and statistical methods for true prevalence estimation provided a good survey tool at lower costs and time when compared to other approaches.     

Differential clustering of Mycoplasma mycoides subsp. mycoides SC strains by PCR-REA of the bgl locus

In order to develop a specific tool differentiating the African field strains of Mycoplasma mycoides subsp. mycoides SC from other potentially less virulent strains, including the vaccine strains, we have developed a PCR followed by a restriction enzyme analysis (PCR–REA). This approach also differentiates the African field strains from the Australian strains and the type strain PG1. The genomic marker detected by the PCR–REA is based on a single nucleotide change in the bgl gene that codes for 6-phospho-β-glucosidase (Bgl), an enzyme that is involved in sugar metabolism.     

Influence of soil water on stress–strain behaviour of a compacting soil in semi-arid Kenya

Depending on the top and subsoil textures, semi-arid soils exhibit cohesive and frictional properties that are associated with the relatively high soil strength, bulk density and penetration resistance. The objective of this study was to gain the knowledge of mechanical properties of the compacting chromic luvisols in order to improve the design of tillage tools. Therefore, we applied critical state soil mechanics to study the stress–strain behaviour of the luvisols using triaxial tests under laboratory conditions. Field investigations involved random collection of undisturbed soil samples which were subjected to triaxial testing first by isotropic consolidation and compression and then triaxial shearing. Plots of deviatoric stress against axial strain were made to determine the soil shear strengths at the critical states over different soil water levels and the two soil depths of 0–20 cm for the plough and 20–40 cm for the hard pan layers, respectively. An exponential model used to fit the deviatoric stress–axial strain test data accurately predicted the trends. Soil water significantly influenced the shear strength, cohesion (c′) and internal angle of friction (′) and hence the mechanical behaviour of the luvisols. The regression equations developed showed that c′ and ′ have quadratic relationships with soil water. The very high clay bonding strength in the subsoil (hard pan) layer resulted in high shear strength, bulk density and penetration resistance values for this soil layer. The increase in shear strength with decreasing water content affected the deviatoric stress–axial strain relationships between the upper and lower plastic limits of the sandy soil. Thus, as the soil dried, the soil ceased to behave in the plastic (ductile flow) manner and thus began to break apart and crumble. The crumbling was indicative of brittle failure. The transition stage from an increase to a decrease in c′ and ′ values with soil water occurred in the soil water content range of 6–10%. Knowledge of stress–strain behaviour of compacting soils is of practical significance in the design of appropriate tillage tools for the specific soil type.     

Is the decline of birds and amphibians in a steppe lake of northern Patagonia a consequence of limnological changes following fish introduction?

• 1. Laguna Blanca, in Laguna Blanca National Park, is a lake in Patagonia which has been designated as a Ramsar site since 1971 because of bird diversity and abundance and importance for nesting, particularly for the black neck swan, Cygnus melanocoryphus. It is also valued for its populations of endemic amphibians, Atelognathus patagonicus and Atelognathus praebasalticus.
• 2. Avian and amphibian populations have decreased dramatically in recent years. Percichthys colhuapiensis, Percichthys trucha (Pisces, Percichthyidae), Salmo trutta and Oncorhynchus mykiss (Pisces, Salmonidae) were introduced into Laguna Blanca in 1965. Since 1986, no Atelognathus frogs have been found. The abundance of swans and coots, which are strongly associated with macrophytes for nesting and feeding, has diminished drastically, whereas piscivorous birds have increased.
• 3. The fishless condition of some neighbouring small lakes with abundant pond weeds, aquatic birds and endemic amphibians, was assessed in order to compare the physical and chemical characteristics and the quantitative composition of the benthos among lakes. Fish presence at Laguna Blanca and its absence at El Burro, Antiñir and Jabón lakes, were confirmed. Compared with previous results, it seems that the abundance of Amphipoda (Hyalella), Copepoda and Cladocera at Laguna Blanca has decreased, while Acari has increased and Notostraca has disappeared. Water transparency has diminished in Laguna Blanca and now is lower than that of fishless lakes.
• 4. P. colhuapiensis were captured only in Laguna Blanca, with the highest captures in the littoral zone. The population shows rapid individual growth in the early years and an absence of fish older than 6 years. The preponderance of benthos and the presence of macrophytes in the gut contents of adult P. colhuapiensis appear to indicate that they are important consumers of these resources.
• 5. This paper concludes that fish introduction in Laguna Blanca led to a complex trophic cascade effect (fish predation on tadpoles, fish competition for avian food, bottom disturbance, zooplankton reduction) producing deleterious effects on the amphibian and bird populations.

Copyright © 2006 John Wiley & Sons, Ltd.     

Molecular characterization and diagnostics of stubby root and virus vector nematodes of the family Trichodoridae (Nematoda: Triplonchida) using ribosomal RNA genes

Plant parasitic nematodes of the family Trichodoridae cause substantial yield losses in many agricultural crops. Rapid and accurate identification of trichodorids to the species level is critical for selection of appropriate measures for control. This study analysed 99 sequences of the D2–D3 expansion segments of the 28S rRNA gene and 131 sequences of the 18S rRNA gene from the stubby nematodes belonging to the genera Nanidorus, Paratrichodorus and Trichodorus. Species delimiting was based on the integration of morphological identification, which is not provided in the present article, and molecular‐based phylogenetic inference and sequence analysis. Twenty‐two valid species and several species complexes were identified among nematodes included in the analysis. PCR‐RFLPs of the partial 18S rDNA and the D2–D3 expansion segments of the 28S rDNA were tested and proposed for identification of these nematodes. Gel PCR‐RFLP profiles and tables with restriction fragment lengths for several diagnostic enzymes are provided for identification. Some problems of taxonomy and phylogeny of nematodes of the family Trichodoridae are also discussed.     

A perspective on the role of quantitative structure-activity and structure-property relationships in herbicide discovery

BACKGROUND: For the last 15 years the agrochemical industry has focused on using genetic modification to put genes that confer resistance to existing commercial herbicides into crop plants rather than on discovering new herbicides with novel modes of action. The widespread appearance of weeds resistant to those herbicides is now causing the industry to revive their herbicide discovery programs. RESULTS: Elucidation of quantitative structure–activity relationships (QSARs) played a major role in the discovery and development of existing commercial herbicides, but the advent of genetically modified crops has caused published work (at least) in the area to drift from the industrial arena into academic studies. The focus has also turned inward, to refining models for established herbicide targets instead of elucidating new ones. CONCLUSION: This perspective highlights the importance of QSARs and quantitative structure–property relationships (QSPRs) to herbicide discovery in an historical context and provides some guidance as to how they might profitably be applied going forward. Copyright © 2011 Society of Chemical Industry     

The structure-activity relationship in herbicidal monosubstituted sulfonylureas

BACKGROUND: The herbicide sulfonylurea (SU) belongs to one of the most important class of herbicides worldwide. It is well known for its ecofriendly, extreme low toxicity towards mammals and ultralow dosage application. The original inventor, G Levitt, set out structure–activity relationship (SAR) guidelines for SU structural design to attain superhigh bioactivity. A new approach to SU molecular design has been developed. RESULTS: After the analysis of scores of SU products by X‐ray diffraction methodology and after greenhouse herbicidal screening of 900 novel SU structures synthesised in the authors' laboratory, it was found that several SU structures containing a monosubstituted pyrimidine moiety retain excellent herbicidal characteristics, which has led to partial revision of the Levitt guidelines. CONCLUSIONS: Among the novel SU molecules, monosulfuron and monosulfuron‐ester have been developed into two new herbicides that have been officially approved for field application and applied in millet and wheat fields in China. A systematic structural study of the new substrate–target complex and the relative mode of action in comparison with conventional SU has been carried out. A new mode of action has been postulated. Copyright © 2011 Society of Chemical Industry     

Human-carnivore conflict in China: a review of current approaches with recommendations for improved management

Human-wildlife conflict (HWC) is a conservation concern that increasingly threatens the continued existence of some of the world's most endangered species. With an increase in human population, urban sprawl and subsequent encroachment on wild land, human and wildlife interaction has become inevitable. In the majority of cases, this interaction results in a negative outcome for humans, wildlife or both. In China, these key elements, along with a decrease in wild prey species, have resulted in the expansion of HWC encounters, and the need for alleviating this conflict has become a conservation priority. Loss of human life, livestock and/or crops is most often the catalysts that fuel HWC. Techniques to alleviate conflict around the world have included preventative measures and mitigation techniques, such as financial compensation and other incentive programs. Both types of measures have had variable success. We review the current status of human-carnivore conflict management in China, and, drawing lessons from around the globe, we make recommendations for improving conservation management in China. For example, an increase in law enforcement in nature reserves is vital to reducing human disturbance in prime carnivore habitat, thereby reducing conflict encounters. Also, modifications to current wildlife compensation programs, so that they are linked with preventative measures, will ensure that moral hazards are avoided. Furthermore, investigating the potential for a community self-financed insurance scheme to fund compensation and increasing efforts to restore wild prey populations will improve the outcome for wildlife conservation. Ultimately, HWC management in China will greatly benefit from an integrative approach.     

Anticipating the species jump: surveillance for emerging viral threats

Zoonotic disease surveillance is typically triggered after animal pathogens have already infected humans. Are there ways to identify high‐risk viruses before they emerge in humans? If so, then how and where can identifications be made and by what methods? These were the fundamental questions driving a workshop to examine the future of predictive surveillance for viruses that might jump from animals to infect humans. Virologists, ecologists and computational biologists from academia, federal government and non‐governmental organizations discussed opportunities as well as obstacles to the prediction of species jumps using genetic and ecological data from viruses and their hosts, vectors and reservoirs. This workshop marked an important first step towards envisioning both scientific and organizational frameworks for this future capability. Canine parvoviruses as well as seasonal H3N2 and pandemic H1N1 influenza viruses are discussed as exemplars that suggest what to look for in anticipating species jumps. To answer the question of where to look, prospects for discovering emerging viruses among wildlife, bats, rodents, arthropod vectors and occupationally exposed humans are discussed. Finally, opportunities and obstacles are identified and accompanied by suggestions for how to look for species jumps. Taken together, these findings constitute the beginnings of a conceptual framework for achieving a virus surveillance capability that could predict future species jumps.