A Comparison of Bayesian Methods for Uncertainty Analysis in Hydraulic and Hydrodynamic Modeling

We evaluate and compare the performance of Bayesian Monte Carlo (BMC), Markov chain Monte Carlo (MCMC), and the Generalized Likelihood Uncertainty Estimation (GLUE) for uncertainty analysis in hydraulic and hydrodynamic modeling (HHM) studies. The methods are evaluated in a synthetic 1D wave routing exercise based on the diffusion wave model, and in a multidimensional hydrodynamic study based on the Environmental Fluid Dynamics Code to simulate estuarine circulation processes in Weeks Bay, Alabama. Results show that BMC and MCMC provide similar estimates of uncertainty. The posterior parameter densities computed by both methods are highly consistent, as well as the calibrated parameter estimates and uncertainty bounds. Although some studies suggest that MCMC is more efficient than BMC, our results did not show a clear difference between the performance of the two methods. This seems to be due to the low number of model parameters typically involved in HHM studies, and the use of the same likelihood function. In fact, for these studies, the implementation of BMC results simpler and provides similar results to MCMC. The results of GLUE are, on the other hand, less consistent to the results of BMC and MCMC in both applications. The posterior probability densities tend to be flat and similar to the uniform priors, which can result in calibrated parameter estimates centered in the parametric space.     

Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China

To better understand the diversity of metal resistance genetic determinant from microbes that survived atmetal tailings in northwest of China, a highly elevated level of heavymetal containing region, genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB). It shows that: Mesorhizobium amorphae CCNWGS0123 contains metal transporters from P-type ATPase, CDF (Cation Diffusion Facilitator), HupE/UreJ and CHR (chromate ion transporter) family involved in copper, zinc, nickel as well as chromate resistance and homeostasis. Meanwhile, the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter, assisted with putative CzcD, determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286. The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion, indicating a potential in-site phytoremediation usage in themining tailing regions of China.     

Induced resistance enzymes in wild plants–do ‘early birds’ escape from pathogen attack?

Systemic acquired resistance (SAR) of plants to pathogens is a well-defined phenomenon. The underlying signalling pathways and its application in crop protection are intensively studied. However, most studies are conducted on crop plants or on Arabidopsis as a model plant. The taxonomic distribution of this phenomenon and its dependence on life history are thus largely unknown. We quantified activities of three classes of resistance-related enzymes in 18 plant species to investigate whether plants with varying life histories differ in their investment in disease resistance. Enzyme activities were quantified in untreated plants, and in plants induced with BION, a chemical resistance elicitor. All species showed constitutive activities of chitinase, peroxidase, or glucanase. However, constitutive chitinase activities varied by 30 times, and peroxidase by 50 times, among species. Several species did not respond to the induction treatment, while enzyme activities in other species increased more than threefold after BION application. Plant species differ dramatically in the presence and inducibility of resistance enzymes. This variation could be related to life history: While all resistance enzymes were significantly induced in larger perennial plants that flower during summer, spring geophytes hardly showed inducible resistance. These plants grow in an environment that is characterised by a low-pathogen pressure, and thus may simply ‘escape’ from infection. Our study presents the first comparative data set on resistance-related enzymes in noncultivated plants. The current view on SAR—narrowed by the concentration on cultivated crops—is not sufficient to understand the ecological and evolutionary relevance of this widespread plant trait.     

Tests of landscape influence: nest predation and brood parasitism in fragmented ecosystems

The effects of landscape fragmentation on nest predation and brood parasitism, the two primary causes of avian reproductive failure, have been difficult to generalize across landscapes, yet few studies have clearly considered the context and spatial scale of fragmentation. Working in two river systems fragmented by agricultural and rural-housing development, we tracked nesting success and brood parasitism in > 2500 bird nests in 38 patches of deciduous riparian woodland. Patches on both river systems were embedded in one of two local contexts (buffered from agriculture by coniferous forest, or adjacent to agriculture), but the abundance of agriculture and human habitation within 1 km of each patch was highly variable. We examined evidence for three models of landscape effects on nest predation based on (1) the relative importance of generalist agricultural nest predators, (2) predators associated with the natural habitats typically removed by agricultural development, or (3) an additive combination of these two predator communities. We found strong support for an additive predation model in which landscape features affect nest predation differently at different spatial scales. Riparian habitat with forest buffers had higher nest predation rates than sites adjacent to agriculture, but nest predation also increased with increasing agriculture in the larger landscape surrounding each site. These results suggest that predators living in remnant woodland buffers, as well as generalist nest predators associated with agriculture, affect nest predation rates, but they appear to respond at different spatial scales. Brood parasitism, in contrast, was unrelated to agricultural abundance on the landscape, but showed a strong nonlinear relationship with farm and house density, indicating a critical point at which increased human habitat causes increased brood parasitism. Accurate predictions regarding landscape effects on nest predation and brood parasitism will require an increased appreciation of the multiple scales at which landscape components influence predator and parasite behavior.     

Ecological opportunity and phenotypic plasticity interact to promote character displacement and species coexistence

We investigated the roles of resource availability and phenotypic plasticity in promoting ecological character displacement (i.e., trait evolution stemming from resource competition between species). Because ecological character displacement generates new populations that differ in resource use, this process should only occur when exploitable resources are available. We tested this hypothesis in two species of spadefoot toads (Spea bombifrons and S. multiplicata) whose tadpoles use phenotypic plasticity to develop into either an omnivore morph, which specializes on detritus, or a physically distinctive carnivore morph, which specializes on shrimp. Both species grow best on shrimp, but when reared together, S. bombifrons outcompetes S. multiplicata for shrimp and S. multiplicata outcompetes S. bombifrons for detritus. We found that when each species occurred alone in the field, they produced similar proportions of omnivores and carnivores. When the two species occurred together, however, they underwent ecological character displacement in larval development, with S. multiplicata producing mostly omnivores, and S. bombifrons producing mostly carnivores. We combined observations of natural populations with experiments to evaluate whether such character displacement was only possible when both shrimp and detritus were relatively abundant. Mixed-species ponds contained abundant detritus and shrimp, in contrast with nearby pure-species ponds, which were deficient in one resource. Experiments revealed that S. multiplicata competed poorly when detritus was rare and that S. bombifrons competed poorly when shrimp was rare. In nature, when one of these two resources was scarce, one species was missing, perhaps through competitive exclusion by the species that was the superior competitor for the remaining resource. Thus, ecological character displacement and, therefore, coexistence of close competitors, was only possible when diverse resources were available. Finally, even if exploitable resources are available, character displacement is not guaranteed to transpire if species cannot utilize such resources expeditiously. Phenotypic plasticity provides a general and important mechanism for facilitating resource partitioning. Thus, by facilitating shifts in resource use, phenotypic plasticity and ecological opportunity may often interact to promote divergence and coexistence of competitors.     

Accumulation of weathered polycyclic aromatic hydrocarbons (PAHs) by plant and earthworm species

Experiments were conducted to assess the bioavailability of polyclycic aromatic hydrocarbons (PAHs) in soil from a Manufactured Gas Plant site. Three plant species were cultivated for four consecutive growing cycles (28 days each) in soil contaminated with 36.3 microg/g total PAH. During the first growth period, Cucurbita pepo ssp. pepo (zucchini) tissues contained significantly greater quantities of PAHs than did Cucumis sativus (cucumber) and Cucurbita pepo ssp. ovifera (squash). During the first growth cycle, zucchini plants accumulated up to 5.47 times more total PAH than did the other plants, including up to three orders of magnitude greater levels of the six ring PAHs. Over growth cycles 2-4, PAH accumulation by zucchini decreased by 85%, whereas the uptake of the contaminants by cucumber and squash remained relatively constant. Over all four growth cycles, the removal of PAHs by zucchini was still twice that of the other species. Two earthworm species accumulated significantly different amounts of PAH from the soil; Eisenia foetida and Lumbricus terrestris contained 0.204 and 0.084 microg/g total PAH, respectively, but neither species accumulated measurable quantities 5 or 6 ring PAHs. Lastly, in abiotic desorption experiments with an aqueous phase of synthetically prepared organic acid solutions, the release of 3 and 4 ring PAHs from soil was unaffected by the treatments but the desorption of 5-6 ring constituents was increased by up to two orders of magnitude. The data show that not only is the accumulation of weathered PAHs species-specific but also that the bioavailability of individual PAH constituents is highly variable.     

Possible chemical causes of skeletal deformities in grey heron nestlings (Ardea cinerea) in North Nottinghamshire, UK

Dead and deformed grey heron (Ardea cinerea) chicks were reported at a large heronry in North Nottinghamshire, UK between 1996 (when systematic visits to the heronry started) and 2002. Many of the birds died for no obvious reason but deformities in others included multiple fractures of the tarsus and tibia and metacarpal bones (angel wings). This study aimed to investigate possible chemical causes of these deformities. Analysis of eggs and nestling tissue for a range of metals showed no levels of concern and no significant differences between unaffected and deformed birds. However, the levels of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) detected in affected heron nestlings in 2002 and in eggs taken from nests in 2003 were sufficiently high to suggest that this may be the underlying cause of the deformities, possibly due to effects on deposition of calcium in bone. Further work is underway to identify where the parent birds of the affected nestlings are feeding and identify the possible source of the pollution.     

Analysing selected VVOCs in indoor air with solid phase microextraction (SPME): a case study

A multi-storey building with great diversity of room use was monitored after extensive renovation to remove mould growth secondary to a leaky roof. Tests for volatile organic compounds (VOC) with activated charcoal showed a successfully renovation. Solid phase microextraction (SPME) for detection of selected very volatile organic compounds (VVOCs) revealed indoor air concentrations ranging from 550 to 4,600 microg m(-3). The SPME technique also successfully detected emissions from working and building materials and documented the results of remedial measures in offices. The prior and current use of acetone, methyl acetate and 2-methylpentane within the building resulted in their elevated concentrations in other building floors.     

Polychlorinated biphenyls (PCBs) in soils of the Moscow region: concentrations and small-scale distribution along an urban-rural transect

In soils of the Moscow region, we examined PCB concentrations in bulk samples and aggregate fractions. Topsoils under grassland and forest at five locations along a southeast-bound transect from Moscow and at a northeastern background location (grassland only) were analysed. We collected aggregates >1 cm and fractionated them into interior and exterior portions and also analysed the remaining soil without the aggregates >1 cm. The concentrations of the sum of 17 PCBs (sigma17PCBs) in 35 bulk soil samples ranged from 3.1 to 42 microg kg(-1). This was 48-61% of the sigma33PCBs determined in 23 selected samples. The congeners 138(+158), 101 and 52 were most abundant. All PCB concentrations and the degree of chlorination declined with increasing distance from Moscow. The PCBs were accumulated in the aggregate exterior (on average 146% of the sigma17PCBs in bulk soil). We conclude that the ecotoxicological risk of PCBs in soils may not be properly assessed with the conventional bulk soil analysis.     

Safety Evaluation for a Biodiesel Process Using Prion-Contaminated Animal Fat as a Source (6 pp)

Background Due to the bovine spongiform encephalopathy (BSE), specified risk material (SRM) as well as animal meat and bone meal (MBM) are banned from the food and feed chain because of a possible infection with pathogenic prions (PrPSc). Nowadays, prions are widely accepted to be responsible for TSE(transmissible spongiform encephalopathies)-caused illnesses like BSE and scrapie, and especially for the occurrence of the new variant of CJD in humans. Presently, SRM and MBM are burnt under high temperatures to avoid any hazards for humans, animals or the environment. The aim of this study was to evaluate a method using animal fat separated from Category I material which includes SRM and the carcasses of TSE-infected animals, or animals suspected of being infected with TSE, as a source for producing biodiesel by transesterification, analogous to the biodiesel process using vegetable oil. Methods For this purpose, animal fat was spiked with scrapie-infected hamster brain equivalents – as representative for a TSE-infected animal – and the biodiesel manufacturing process was downscaled and performed under lab-scale conditions. Results and Discussion The results analysed by Western blotting showed clearly that almost each single step of the process leads to a significant reduction of the concentration of the pathogenic prion protein (PrPSc) in the main and side-products. Conclusion The data revealed that the biodiesel production, even from material with a high concentration of pathogenic prions, can be considered as safe. Recommendations and Outlook The obtained results indicated that biodiesel produced from prion-contaminated fat was safe under the tested process conditions. However, it has to be pointed out that the results cannot be generalized because a different process control using other conditions may lead to different results and then has to be analysed independently. It is clear that the production of biodiesel from high risk material represents a more economic usage than the combustion of such material.