An improved model for linking phosphorus loads in runoff to climate, soil and agricultural management

Abstract: Soil phosphorus (P) is one of the nutrients that contribute to eutrophication of waterways, algal blooms and damage to coral reefs. Reducing P movement from farm paddock to the broader environment often requires comprehensive, catchment-wide approaches to management. The substantial complexity of the physical and managerial causes of P pollution has led to a role for simulation models in evaluating the efficacy of regulations and management changes. In Queensland, the Reef Plan program (http://www.reefplan.qld.gov.au) addresses issues of sediment, nutrient and pesticide impact on the health and future of the Great Barrier Reef. Some of the associated regulations are concerned with the use of P fertilizer. The HowLeaky? model is one of few biophysical models that represent agricultural management, biophysical conditions and P exports. As reported at MODSIM07, information about P export was added to an existing model of water balance and sediment export (HowLeaky?) to create a useful model of P export from agriculture. However, the predictive power of the model was modest, especially over short periods (e.g. individual days). To improve the predictive power of the model, several changes have been made, including (i) additional empirical functions for estimating the enrichment of total P in sediment, and (ii) additional functions for estimating concentration of soluble P in runoff (mg P/L). Soil adsorption of P (P buffering), which affects the soluble P concentration in runoff, is now estimated from the widely available phosphorus buffering index test (PBI) rather than phosphorus buffering capacity (PBC). Large, high-quality datasets are used to evaluate these relationships. A case study is presented where HowLeaky? has been used to estimate P loads generated at a site in the GBR catchment. The Brigalow Catchment Study is a long-term study of the effects of land clearing and agriculture on the water balance and water quality. It is located in central Queensland, has a subcatchment that is cropped, has representative soils, and is part of the Fitzroy Catchment. HowLeaky? reproduced daily runoff amounts very well, and the revised P model in HowLeaky? was acceptably accurate at predicting daily P loads. Modelling predicted the long-term totals (6 years) of soluble and particulate P export from the field site with less than 50% error. This is a better-than-expected result with an un-calibrated model, as P exports are notoriously difficult to predict

A Cross-Study Transcriptional Analysis of Parkinson's Disease

The study of Parkinson's disease (PD), like other complex neurodegenerative disorders, is limited by access to brain tissue from patients with a confirmed diagnosis. Alternatively the study of peripheral tissues may offer some insight into the molecular basis of disease susceptibility and progression, but this approach still relies on brain tissue to benchmark relevant molecular changes against. Several studies have reported whole-genome expression profiling in post-mortem brain but reported concordance between these analyses is lacking. Here we apply a standardised pathway analysis to seven independent case-control studies, and demonstrate increased concordance between data sets. Moreover data convergence increased when the analysis was limited to the five substantia nigra (SN) data sets; this highlighted the down regulation of dopamine receptor signaling and insulin-like growth factor 1 (IGF1) signaling pathways. We also show that case-control comparisons of affected post mortem brain tissue are more likely to reflect terminal cytoarchitectural differences rather than primary pathogenic mechanisms. The implementation of a correction factor for dopaminergic neuronal loss predictably resulted in the loss of significance of the dopamine signaling pathway while axon guidance pathways increased in significance. Interestingly the IGF1 signaling pathway was also over-represented when data from non-SN areas, unaffected or only terminally affected in PD, were considered. Our findings suggest that there is greater concordance in PD whole-genome expression profiling when standardised pathway membership rather than ranked gene list is used for comparison

NRF2 Activation Restores Disease Related Metabolic Deficiencies in Olfactory Neurosphere-Derived Cells from Patients with Sporadic Parkinson's Disease

Extent: 14p.Background: Without appropriate cellular models the etiology of idiopathic Parkinson’s disease remains unknown. We recently reported a novel patient-derived cellular model generated from biopsies of the olfactory mucosa (termed olfactory neurosphere-derived (hONS) cells) which express functional and genetic differences in a disease-specific manner. Transcriptomic analysis of Patient and Control hONS cells identified the NRF2 transcription factor signalling pathway as the most differentially expressed in Parkinson’s disease. Results: We tested the robustness of our initial findings by including additional cell lines and confirmed that hONS cells from Patients had 20% reductions in reduced glutathione levels and MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)- 2-(4-sulfophenyl)-2H-tetrazolium, inner salt] metabolism compared to cultures from healthy Control donors. We also confirmed that Patient hONS cells are in a state of oxidative stress due to higher production of H2O2 than Control cultures. siRNA-mediated ablation of NRF2 in Control donor cells decreased both total glutathione content and MTS metabolism to levels detected in cells from Parkinson’s Disease patients. Conversely, and more importantly, we showed that activation of the NRF2 pathway in Parkinson’s disease hONS cultures restored glutathione levels and MTS metabolism to Control levels. Paradoxically, transcriptomic analysis after NRF2 pathway activation revealed an increased number of differentially expressed mRNAs within the NRF2 pathway in L-SUL treated Patient-derived hONS cells compared to L-SUL treated Controls, even though their metabolism was restored to normal. We also identified differential expression of the PI3K/AKT signalling pathway, but only post-treatment. Conclusions: Our results confirmed NRF2 as a potential therapeutic target for Parkinson’s disease and provided the first demonstration that NRF2 function was inducible in Patient-derived cells from donors with uniquely varied genetic backgrounds. However, our results also demonstrated that the response of PD patient-derived cells was not co-ordinated in the same way as in Control cells. This may be an important factor when developing new therapeutics.Anthony L. Cook, Alejandra M. Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jiangou Shan, Ratneswary Sutharsan, Chris Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay-Sim and Stephen A. Woo

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

The hydrogeology of the Condamine River alluvial aquifer (Australia) – a critical review

The Condamine plain is an important agricultural zone, with ~118 thousand hectares of irrigated crops. Groundwater pumped from the shallow alluvial aquifer (40-60 GL/yr) accounts for one third of the irrigation water. Sustainable agriculture future implies, among other issues, a reliable supply of groundwater to the farmers, in terms of quality and quantity. The hydrogeology of the shallow Condamine River Alluvium Aquifer (CRAA) was studied for decades in order to provide a management framework and to determine the 'safe yield', as excessive pumping in the past has led to ongoing decline of the water table, up to ~25m in places. Not withstanding the accumulating data and knowledge, the water balance of the aquifer as well as 'safe yield' estimations are still far from being conclusive and has been substantially revised several times during the last decade. The present report, conducted at the University of Southern Queensland (USQ), collates up-to-date hydrogeological knowledge regarding the CRAA, critically evaluates the accepted hydrogeological conventions, highlights puzzling phenomena and recommends needed work, which can be implemented in a rather expeditious and inexpensive fashion, to overcome the existing knowledge gaps. Refining the hydrogeological knowledge regarding the CCRA is timely, as in the last decade there has been a rapid expansion of the CSG industry in vicinity to the Condamine plain, with the aim to extract methane from the underlying layers. The presumed hydrogeological effects of CSG production upon the shallower CRAA have been delineated but are yet to be adequately quantified. It is our view that the hydrogeological knowledge-gaps should be addressed before predictions of CSG activities effects can be made

The hydrogeology of the Condamine River alluvial aquifer, Australia: a critical assessment

The Condamine plain is an important agricultural zone in Australia with prominent irrigated cotton and grain crops. About one third of the irrigation water is pumped from the shallow alluvial aquifer, causing gross aquifer depletion over time. Over the last few decades, various hydrological, hydrochemical, and geological aspects of this aquifer and the overlying floodplain (including soil properties) have been investigated and used to construct the conceptual understanding and numerical models for management of this resource. Yet, the water balance of the aquifer is still far from resolved, and the geological contact between the alluvial sediments and underlying bedrock is yet to be categorically defined, to mention two major uncertainties. This paper collates up-to-date knowledge of different disciplines, critically evaluates the accepted hydrogeological conventions, highlights key knowledge gaps, and suggests strategies for future research. Among recommendations are (1) development of numerical flow and solute transport models for the natural (ie. pre-developed) period, (2) analysis of groundwater for isotopic composition and presence of pesticides, CFCs and PPCPs, and (3) use of stochastic approaches to characterize the hydraulic properties of the alluvial sediments. These and other proposed measures are relevant also to other alluvial aquifers which suffer from similar fundamental uncertainties

Catchment salt balances in the Queensland Murray-Darling Basin, Australia

Catchment salt mass balances and export/import ratios were calculated for 55 gauging stations in nine major catchments across the Queensland Murray–Darling Basin (QMDB), Australia. Salt inputs were comprised of atmospheric, groundwater and inter-basin transfer contributions, while exports were derived from model runs calibrated to streamflow data and flow-salt relationships. Catchment atmospheric salt inputs were larger than groundwater inputs in the major catchments, with the exception of the Condamine catchment. Across the whole QMDB, the magnitude of atmospheric and groundwater inputs is potentially equal. Average annual streamflow salt export is generally much less than salt input, even when atmospheric inputs alone are considered, and is strongly influenced by episodic, large events. The exceptions to this are some smaller salt-affected upland catchments in the eastern QMDB where flow is more continual (i.e. baseflow occurs) and stream salinity is higher – a result of long-term land use change impacts. Variability in catchment salt export/import ratio (E/I) as a result of different calculation methods for both inputs and outputs creates a wide range in possible E/I for some sites, but trends remain the same. Losses of stream water to floodplains, seepage and extractions in lower portions of catchments leads to significant reductions in E/I with distance downstream. It appears that in general, the natural status of the QMDB is one of salt accumulation and significant hydrologic changes – as represented through salt mass balance calculations – are largely confined to the eastern half of the Basin, although further change may yet express in the landscape

Pesticide behavior, fate, and effects in the Tropics: an overview of the current state of knowledge

This special issue presents a collection of papers covering the environmental fate, effects, and risk of pesticides in tropical environments, which is expected to facilitate improved management of pesticides. Environmental monitoring programs of surface and ground waters in the tropics, including areas of high ecological value, have detected several relatively polar pesticides at concentrations that are of ecological concern. Novel monitoring techniques have the capacity to reveal the spatial and temporal extent of such risks. To best manage these pesticides, their sorption, dissipation rates, leaching, and runoff potential need to be better understood. On these aspects, important insights have been provided by several studies within this issue. Improved understanding of the environmental fate, effects, and risks through studies presented in this special issue is crucial for minimizing the nontarget impacts of pesticides on biodiversity-rich tropical regions

Direct comparison of runoff of residual and knockdown herbicides in sugarcane using a rainfall simulator finds large difference in runoff losses and toxicity relative to diuron

Runoff losses of herbicides have rarely been compared simultaneously under the same conditions. Our aim was to directly compare herbicide runoff losses, normalised for the amount present (relative runoff loads) and in absolute terms. Toxicity and runoff concentrations were combined to provide a risk ranking relative to diuron. Four rainfall simulation trials were conducted in sugarcane in the Great Barrier Reef catchment. Herbicides studied were older PSII residuals (atrazine, ametryn, diuron, hexazinone), alternative residuals (isoxaflutole, imazapic, metribuzin, metolachlor, pendimethalin) and knockdown herbicides (glyphosate, 2,4-D, fluroxypyr) and the tracer bromide (Br). Simulations were conducted two days after spraying, before differences due to half-lives were apparent. Two trials had bare soil and two had sugarcane trash. Herbicide runoff losses and concentrations were closely related to the amount applied, runoff amounts and partitioning coefficients. Relative runoff losses and absolute losses were similar for most older and alternative residual herbicides, 2,4-D and Br. Glyphosate and pendimethalin relative runoff losses were low, due to greater sorption. Isoxaflutole, imazapic, and fluroxypyr are applied at much lower rates and runoff losses were low. Herbicides were lost in the dissolved phase, except pendimethalin. There was a large range in toxicity relative to diuron. There is a range of herbicide choices posing less offsite risk than diuron and ametryn, which have high application rates and high toxicity. Herbicide choice should consider application rate, runoff losses, sorption, and toxicity