Comparison of three vegetation monitoring methods: Their relative utility for ecological assessment and monitoring

Vegetation cover and composition are two indicators commonly used to monitor terrestrial ecosystems. These indicators are currently quantified with a number of different methods. The interchangeability and relative benefits of different methods have been widely discussed in the literature, but there are few published comparisons that address multiple criteria across a broad range of grass- and shrub-dominated communities, while keeping sampling effort (time) approximately constant. This study compared the utility of three field sampling methods for ecological assessment and monitoring: line-point intercept, grid-point intercept, and ocular estimates. The criteria used include: (1) interchangeability of data, (2) precision, (3) cost, and (4) value of each method based on its potential to generate multiple indicators. Foliar cover by species was measured for each method in five plant communities in the Chihuahuan Desert. Line- and grid-point intercept provide similar estimates of species richness which were lower than those based on ocular estimates. There were no differences in the precision of the number of species detected. Estimates of foliar cover with line- and grid-point intercept were similar and significantly higher than those based on ocular estimates. Precision of cover estimates with line-point intercept was higher than for ocular estimates. Time requirements for the three methods were similar, despite the fact that the point-based methods included cover estimates for all canopy layers and the soil surface, while the ocular estimates included only the top canopy layer. Results suggest that point-based methods provide interchangeable data with higher precision than ocular estimates. Moreover these methods can be used to generate a much greater number of indicators that are more directly applicable to a variety of monitoring objectives, including soil erosion and wildlife habitat.     

The epidemiology and public health importance of toxocariasis: A zoonosis of global importance

Toxocariasis, caused by infection with larvae of Toxocara canis, and to a lesser extent by Toxocara cati and other ascaridoid species, manifests in humans in a range of clinical syndromes. These include visceral and ocular larva migrans, neurotoxocariasis and covert or common toxocariasis. Toxocara canis is one of the most widespread public health and economically important zoonotic parasitic infections humans share with dogs, cats and wild canids, particularly foxes. This neglected disease has been shown through seroprevalence studies to be especially prevalent among children from socio-economically disadvantaged populations both in the tropics and sub-tropics and in industrialised nations. Human infection occurs by the accidental ingestion of embryonated eggs or larvae from a range of wild and domestic paratenic hosts. Most infections remain asymptomatic. Clinically overt infections may go undiagnosed, as diagnostic tests are expensive and can require serological, molecular and/or imaging tests, which may not be affordable or available. Treatment in humans varies according to symptoms and location of the larvae. Anthelmintics, including albendazole, thiabendazole and mebendazole may be given together with anti-inflammatory corticosteroids. The development of molecular tools should lead to new and improved strategies for the treatment, diagnosis and control of toxocariasis and the role of other ascaridoid species in the epidemiology of Toxocara spp. Molecular technologies may also help to reveal the public health importance of T. canis, providing new evidence to support the implementation of national control initiatives which have yet to be developed for Toxocara spp. A number of countries have implemented reproductive control programs in owned and stray dogs to reduce the number of young dogs in the population. These programs would positively impact upon T. canis transmission since the parasite is most fecund and prevalent in puppies. Other control measures for T. canis include the regular and frequent anthelmintic treatment of dogs and cats, starting at an early age, education and enforcement of laws for the disposal of canine faeces, dog legislation and personal hygiene. The existence of wild definitive and paratenic hosts complicates the control of T. canis. Increasing human and dog populations, population movements and climate change will all serve to increase the importance of this zoonosis. This review examines the transmission, diagnosis and clinical syndromes of toxocariasis, its public health importance, epidemiology, control and current research needs.     

Prioritizing causal disease genes using unbiased genomic features

Background

Cardiovascular disease (CVD) is the leading cause of death in the developed world. Human genetic studies, including genome-wide sequencing and SNP-array approaches, promise to reveal disease genes and mechanisms representing new therapeutic targets. In practice, however, identification of the actual genes contributing to disease pathogenesis has lagged behind identification of associated loci, thus limiting the clinical benefits.

Results

To aid in localizing causal genes, we develop a machine learning approach, Objective Prioritization for Enhanced Novelty (OPEN), which quantitatively prioritizes gene-disease associations based on a diverse group of genomic features. This approach uses only unbiased predictive features and thus is not hampered by a preference towards previously well-characterized genes. We demonstrate success in identifying genetic determinants for CVD-related traits, including cholesterol levels, blood pressure, and conduction system and cardiomyopathy phenotypes. Using OPEN, we prioritize genes, including FLNC, for association with increased left ventricular diameter, which is a defining feature of a prevalent cardiovascular disorder, dilated cardiomyopathy or DCM. Using a zebrafish model, we experimentally validate FLNC and identify a novel FLNC splice-site mutation in a patient with severe DCM.

Conclusion

Our approach stands to assist interpretation of large-scale genetic studies without compromising their fundamentally unbiased nature.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0534-8) contains supplementary material, which is available to authorized users.     

A simple model of the hydrophobic effect for molecular simulation of interfacial phenomena

A coarse-grained model for simulation of interfacial phenomena in aqueous systems has been developed. The model captures the hydrophobic effect by only considering the structure and cohesiveness of water. Monte Carlo (MC) simulations of water-oil mixtures show that low concentrations of oil are solvated with little perturbation of the hydrogen bonding network structure of the water, while high concentrations of oil are excluded altogether. Analysis of the water structure in the simulations indicates that the water molecules maintain close to four coordination in the presence of solutes and the distribution of bond angles is not markedly affected by the presence of solutes. MC simulations of an alkane oligomer in water and a poly(ethylene oxide) (PEO) oligomer in water indicate that the chains are quite flexible and also do not perturb the network structure of the water phase.     

Human organisms begin to exist at fertilization

Eugene Mills has recently argued that human organisms cannot begin to exist at fertilization because the evidence suggests that egg cells persist through fertilization and simply turn into zygotes. He offers two main arguments for this conclusion: that ‘fertilized egg’ commits no conceptual fallacy, and that on the face of it, it looks as though egg cells survive fertilization when the process is watched through a microscope. We refute these arguments and offer several reasons of our own to think that egg cells do not survive fertilization, appealing to various forms of essentialism regarding persons, fission cases, and a detailed discussion of the biological facts relevant to fertilization and genetics. We conclude that it is plausible, therefore, that human organisms begin to exist at fertilization – or, at the very least, that there are grounds for thinking that they existed as zygotes which do not apply to the prior egg cells. While this does not entail that human persons begin to exist at this point, it nevertheless has considerable significance for this latter question.     

Chemical suppression of a genetic mutation in a zebrafish model of aortic coarctation

Conventional drug discovery approaches require a priori selection of an appropriate molecular target, but it is often not obvious which biological pathways must be targeted to reverse a disease phenotype. Phenotype-based screens offer the potential to identify pathways and potential therapies that influence disease processes. The zebrafish mutation gridlock (grl, affecting the gene hey2) disrupts aortic blood flow in a region and physiological manner akin to aortic coarctation in humans. Here we use a whole-organism, phenotype-based, small-molecule screen to discover a class of compounds that suppress the coarctation phenotype and permit survival to adulthood. These compounds function during the specification and migration of angioblasts. They act to upregulate expression of vascular endothelial growth factor (VEGF), and the activation of the VEGF pathway is sufficient to suppress the gridlock phenotype. Thus, organism-based screens allow the discovery of small molecules that ameliorate complex dysmorphic syndromes even without targeting the affected gene directly.     

SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data

Background  

Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles.     

Invader–invader interactions in relation to environmental heterogeneity leads to zonation of two invasive amphipods, Dikerogammarus villosus (Sowinsky) and Gammarus tigrinus Sexton: amphipod pilot species project (AMPIS) report 6

As biological invasions continue, interactions occur not only between invaders and natives, but increasingly new invaders come into contact with previous invaders. Whilst this can lead to species replacements, co-existence may occur, but we lack knowledge of processes driving such patterns. Since environmental heterogeneity can determine species richness and co-existence, the present study examines habitat use and its mediation of the predatory interaction between invasive aquatic amphipods, the Ponto-Caspian Dikerogammarus villosus and the N. American Gammarus tigrinus. In the Dutch Lake IJsselmeer, we found broad segregation of D. villosus and G. tigrinus by habitat type, the former predominating in the boulder zone and the latter in the soft sediment. However, the two species co-exist in the boulder zone, both on the short and longer terms. We used an experimental simulation of habitat heterogeneity and show that both species utilize crevices, different sized holes in a plastic grid, non-randomly. These amphipods appear to optimise the use of holes with respect to their ‘C-shape’ body size. When placed together, D. villosus adults preyed on G. tigrinus adults and juveniles, while G. tigrinus adults preyed on D. villosus juveniles. Juveniles were also predators and both species were cannibalistic. However, the impact on G. tigrinus of the superior intraguild predator, D. villosus, was significantly reduced where experimental grids were present as compared to absent. This mitigation of intraguild predation between the two species in complex habitats may explain the co-existence of these two invasive species.