Phytoremediation of polycyclic aromatic hydrocarbons in soil: part I. Dissipation of target contaminants

Phytoremediation has been demonstrated to be a viable cleanup alternative for soils contaminated with petroleum products. This study evaluated the application of phytoremediation to soil from a manufactured gas plant (MGP) site with high concentrations of recalcitrant, polycyclic aromatic hydrocarbons (PAHs). Two greenhouse studies investigated the potential dissipation and plant translocation of PAHs by fescue (Festuca arundinacea) and switchgrass (Panicum virgatum) in the first experiment and zucchini (Curcubita pepo Raven) in the second. The MGP soil was highly hydrophobic and initially inhibited plant growth. Two unplanted controls were established with and without fertilization. In the first experiment, concentrations of PAHs decreased significantly in all treatments after 12 mo. Plant biomass and microbial numbers were statistically equivalent among plant species. PAH concentrations in plant biomass were negligible for fescue and switchgrass. In the second experiment, zucchini enhanced the dissipation of several PAHs after 90 d of treatment when compared to the unvegetated soil. Plant tissue concentrations of PAHs were not elevated in the zucchini roots and shoots, and PAHs were not detectable in the fruit.     

Impact of microbial/plant interactions on the transformation of polycyclic aromatic hydrocarbons in rhizosphere of Festuca arundinacea

The promotion of polycyclic aromatic hydrocarbon (PAH) degradation was demonstrated in the rhizosphere of Festuca arundinacea with Pseudomonas fluorescens. P. fluorescens 5RL more significantly interacted with salicylate and dextrose in the agar containing tall fescue than agar without plant roots. Although the presence of tall fescue did not promote catabolic enzyme induction in the absence of salicylate, an increase in dioxygenase activity relative to no plant controls implies that this plant may enhance the degradation of PAHs or facilitate the genotypes that are capable of transforming PAH in the rhizosphere.     

Phytoremediation of polycyclic hydrocarbon contaminated soil: part II. Impact on ecotoxicity

Several biological assays were used to evaluate the toxic effects of contaminants in soil after phytoremediation. During the treatment process, significant decreases in overall toxicity were observed. Specifically, earthworm survivability and lettuce germination increased over the study period. Microbial respiration improved, but only in planted treatments. Toxicity and total polycyclic aromatic hydrocarbon concentrations showed some correlation, but the relationships generally were not significant. Soil moisture was less of a predictor for biological responses. The presence of plants did not provide a clear advantage for improving toxicity compared to unplanted treatments.     

Effect of Phosphorylation on EGFR Dimer Stability Probed by Single-Molecule Dynamics and FRET/FLIM

Deregulation of epidermal growth factor receptor (EGFR) signaling has been correlated with the development of a variety of human carcinomas. EGF-induced receptor dimerization and consequent trans- auto-phosphorylation are among the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change that consequently unfolds an ectodomain loop required for dimerization indirectly. It may also induce important allosteric changes in the cytoplasmic domain. Despite extensive knowledge on the physiological activation of EGFR, the effect of targeted therapies on receptor conformation is not known and this particular aspect of receptor function, which can potentially be influenced by drug treatment, may in part explain the heterogeneous clinical response among cancer patients. Here, we used Förster resonance energy transfer/fluorescence lifetime imaging microscopy (FRET/FLIM) combined with two-color single-molecule tracking to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKIs) and phosphatase-based manipulation of EGFR phosphorylation on live cells. The distribution of dimer on-times was fitted to a monoexponential to extract dimer off-rates (k_off). Our data show that pretreatment with gefitinib (active conformation binder) stabilizes the EGFR ligand-bound homodimer. Overexpression of EGFR-specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. No significant difference in the k_off of the dimer could be detected when an anti-EGFR antibody (425 Snap single-chain variable fragment) that allows for dimerization of ligand-bound receptors, but not phosphorylation, was used. These results suggest that both the conformation of the extracellular domain and phosphorylation status of the receptor are involved in modulating the stability of the dimer. The relative fractions of these two EGFR subpopulations (interacting versus free) were obtained by a fractional-intensity analysis of ensemble FRET/FLIM images. Our combined imaging approach showed that both the fraction and affinity (surrogate of conformation at a single-molecule level) increased after gefitinib pretreatment or DEP-1 phosphatase overexpression. Using an EGFR mutation (I706Q, V948R) that perturbs the ability of EGFR to dimerize intracellularly, we showed that a modest drug-induced increase in the fraction/stability of the EGFR homodimer may have a significant biological impact on the tumor cell’s proliferation potential.     

Ecological processes in urban landscapes: mechanisms influencing the distribution and activity of insectivorous bats

Urbanisation affects indigenous fauna in many ways; some species persist and even increase in urban areas, whereas others are lost. The causative mechanisms determining changes in distributions and community structure remain elusive. We investigated three hypothesized mechanisms, which influence success or failure of the insectivorous bat assemblage across the urban landscape of Sydney, Australia; landscape heterogeneity (diversity of land uses), productivity (as indexed by landscape geology) and trait diversity. We present data on species richness and activity (bat passes per night) collected systematically using ultrasonic bat detectors from randomly selected landscapes (each 25 km²). Landscapes were categorized into classes including ‘urban’, ‘suburban’ and ‘vegetated’, where suburban sites were additionally stratified based on geology, as a proxy for productivity. Four landscape elements were sampled within each landscape, including remnant bushland (>2 ha), riparian areas, open space/parkland and residential/built space. We found that there was significantly greater bat activity and more species of bat in areas on fertile shale geologies (p<0.05), supporting the productivity, rather than the heterogeneity hypothesis. Within landscapes, there was no significant effect of the landscape element sampled, although bushland and riparian sites recorded greater bat activity than open space or backyard sites. Using general linear mixed models we found bat activity and species richness were sensitive to landscape geology and increasing housing density at a landscape scale. Using an RLQ analysis a significant relationship was found between these variables and species traits in structuring the community present (p<0.01). Specifically, open‐adapted bats were associated with areas of greater housing density, while clutter‐adapted bats were uncommon in urban areas and more associated with greater amounts of bushland in the landscape. Overall we found greater support for the productivity and traits hypotheses, rather than the heterogeneity hypothesis. The degree of urbanisation and amount of bushland remaining, in combination with landscape geology, influenced bat activity and mediated the trait response. Our findings reflect global trends of species diversity and abundance in urban landscapes, suggesting that processes affecting bat species distribution in urban ecosystems may be predictable at a landscape scale.     

Highly active antiretroviral therapy drug combination induces oxidative stress and mitochondrial dysfunction in immortalized human blood-brain barrier endothelial cells

The era of highly active antiretroviral therapy (HAART) has controlled AIDS and its related disorders considerably; however, the prevalence of HIV-1-associated neurocognitive disorders has been on the rise in the post-HAART era. In view of these developments, we investigated whether a HAART drug combination of 3'-azido-2',3'-deoxythymidine (AZT) and indinavir (IDV) can alter the functionality of the blood-brain barrier (BBB) endothelial cells, thereby exacerbating this condition. The viability of hCMEC/D3 cells (in vitro model of BBB) that were exposed to these drugs was significantly reduced after 72h treatment, in a dose-dependent manner. Reactive oxygen species were highly elevated after the exposure, indicating that mechanisms that induce oxidative stress were involved. Measures of oxidative stress parameters, such as glutathione and malondialdehyde, were altered in the treated groups. Loss of mitochondrial membrane potential, as assessed by fluorescence microscopy and decreased levels of ATP, indicated that cytotoxicity was mediated through mitochondrial dysfunction. Furthermore, AZT+IDV treatment caused apoptosis in endothelial cells, as assessed by the expression of cytochrome c and procaspase-3 proteins. Pretreatment with the thiol antioxidant N-acetylcysteine amide reversed some of the pro-oxidant effects of AZT+IDV. Results from our in vitro studies indicate that the AZT+IDV combination may affect the BBB in HIV-infected individuals treated with HAART drugs.     

The P2X1 receptor and platelet function

Extracellular nucleotides are ubiquitous signalling molecules, acting via the P2 class of surface receptors. Platelets express three P2 receptor subtypes, ADP-dependent P2Y1 and P2Y12 G-protein-coupled receptors and the ATP-gated P2X1 non-selective cation channel. Platelet P2X1 receptors can generate significant increases in intracellular Ca²⁺, leading to shape change, movement of secretory granules and low levels of α_IIbβ₃ integrin activation. P2X1 can also synergise with several other receptors to amplify signalling and functional events in the platelet. In particular, activation of P2X1 receptors by ATP released from dense granules amplifies the aggregation responses to low levels of the major agonists, collagen and thrombin. In vivo studies using transgenic murine models show that P2X1 receptors amplify localised thrombosis following damage of small arteries and arterioles and also contribute to thromboembolism induced by intravenous co-injection of collagen and adrenaline. In vitro, under flow conditions, P2X1 receptors contribute more to aggregate formation on collagen-coated surfaces as the shear rate is increased, which may explain their greater contribution to localised thrombosis in arterioles compared to venules within in vivo models. Since shear increases substantially near sites of stenosis, anti-P2X1 therapy represents a potential means of reducing thrombotic events at atherosclerotic plaques.     

Stream Nitrate Responds Rapidly to Decreasing Nitrate Deposition

Ecosystem acidification and eutrophication resulting from increased deposition of dissolved inorganic nitrogen (DIN) are issues of increasing global concern. Consequently, costly policy decisions are being implemented to decrease nitrogen oxide (NO _x ) emissions. Although declining DIN deposition along with rapid declines of DIN in surface waters have been reported in parts of Europe, the same observation is just emerging in North America. Here we find a significant decline in bulk deposition NO₃ ⁻ during the later part of a 28-year record in southcentral Ontario, Canada. Despite high N retention and substantial inter-annual variability in the long-term record due to periods of drought, we find significant declines in annual NO₃ ⁻ concentrations and export at six out of 11 streams that drain upland-dominated catchments. In contrast, five streams draining primarily wetland-dominated catchments with lower levels of NO₃ ⁻ show no decreasing trend in NO₃ ⁻ concentration or export. The rapid response in stream NO₃ ⁻ to declining atmospheric inputs was observed at sites with historically moderate inputs of DIN (~870 mg m⁻² y⁻¹) in bulk deposition. Topographic features such as slope, and related catchment features including wetland cover, appear to influence which catchments will respond positively to declining DIN deposition. These findings force us to revise our original conceptualization of the N saturation status of these catchments.     

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Background

Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.

Results

Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.

Conclusions

When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.