A tool for estimating Best Management Practice effectiveness in Arkansas

Increased nutrient and sediment losses from expanding agricultural practices and urban development in Arkansas are important environmental concerns. Best Management Practices (BMPs) are being implemented to lessen the effects of these developments on existing water bodies. There is, however, insufficient scientific base as to the effectiveness of these practices. A number of studies have been conducted in recent years to determine BMP effectiveness. Data from these studies can only be reliably used for the individual site from which they were obtained. When considered collectively, these data comprise quantitative effectiveness over a wide range of conditions and can thus be used to provide reliable estimates of BMP effectiveness. This study develops a tool for estimating BMP effectiveness, based on accumulation and analyses of data reported in previous studies, with a focus on site conditions and management interventions in Arkansas. This study incorporates data from a variety of regions in the southeastern U.S., which have site conditions and management similar to those in Arkansas. Developed within Microsoft® Access© from a pre-existing BMP characterization tool, this tool will be made accessible to local and state agencies and will aid rural and urban planners in developing management solutions for nutrients and sediment control. The tool describes individual BMPs in detail and gives site-specific estimates of their long-term effectiveness in sediment and nutrient control

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression

Nutrient dynamics of agricultural drainage ditches in the Hoagland Ditch watershed in northern Indiana

Drainage ditches are used extensively in the Midwest to remove standing water from poorly drained agricultural fields. However, drainage ditches are thought to expedite downstream nutrient transport and prevent denitrification within soils. Little research has currently been performed on the nutrient dynamics within Midwestern ditches, however, studies point to agricultural and drainage in the Midwest as the source of the hypoxia in the Gulf of Mexico. This study focused on seasonal nutrient dynamics within three agricultural drainage ditches with different management practices (dredging, vegetated, and unvegetated) in the Hoagland Ditch watershed in northern Indiana. Short-term nutrient injections of nitrate, phosphate, and ammonium were performed in the ditches to determine nutrient uptake length (Sw) during spring and fall conditions. Injections of phosphate and ammonium into the vegetated ditched yielded shorter Sw than in the nonvegetated ditch, indicating greater retention and processing of nutrients in the vegetated ditch. Nitrate uptake was determined to be negligible due to high ambient nitrate concentrations. To determine sediment-nutrient interactions, sediment extractions including equilibrium phosphorus concentration (EPCo), phosphorous sorption index (PSI), and exchangeable phosphorous (Ex-P) were performed. Dredging disturbed the bottom sediments and affected Ex-P, PSI, and EPCo sediment extraction experiments at Robinson Ditch. This ditch experienced increased Ex-P and decreased PSI, possibly due to ditch dredging

Assessing the Impact of Site-Specific BMPs Using a Spatially Explicit, Field-Scale SWAT Model with Edge-of-Field and Tile Hydrology and Water-Quality Data in the Eagle Creek Watershed, Ohio

The Eagle Creek watershed, a small subbasin (125 km2) within the Maumee River Basin, Ohio, was selected as a part of the Great Lakes Restoration Initiative (GLRI) “Priority Watersheds” program to evaluate the effectiveness of agricultural Best Management Practices (BMPs) funded through GLRI at the field and watershed scales. The location and quantity of BMPs were obtained from the U.S. Department of Agriculture-Natural Resources Conservation Service National Conservation Planning (NCP) database. A Soil and Water Assessment Tool (SWAT) model was built and calibrated for this predominantly agricultural Eagle Creek watershed, incorporating NCP BMPs and monitoring data at the watershed outlet, an edge-of-field (EOF), and tile monitoring sites. Input air temperature modifications were required to induce simulated tile flow to match monitoring data. Calibration heavily incorporated tile monitoring data to correctly proportion surface and subsurface flow, but calibration statistics were unsatisfactory at the EOF and tile monitoring sites. At the watershed outlet, satisfactory to very good calibration statistics were achieved over a 2-year calibration period, and satisfactory statistics were found in the 2-year validation period. SWAT fixes parameters controlling nutrients primarily at the watershed level; a refinement of these parameters at a smaller-scale could improve field-level calibration. Field-scale modeling results indicate that filter strips (FS) are the most effective single BMPs at reducing dissolved reactive phosphorus, and FS typically decreased sediment and nutrient yields when added to any other BMP or BMP combination. Cover crops were the most effective single, in-field practice by reducing nutrient loads over winter months. Watershed-scale results indicate BMPs can reduce sediment and nutrients, but reductions due to NCP BMPs in the Eagle Creek watershed for all water-quality constituents were less than 10%. Hypothetical scenarios simulated with increased BMP acreages indicate larger investments of the appropriate BMP or BMP combination can decrease watershed level loads

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci

RATIONALE: Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA. OBJECTIVE: To identify additional AAA risk loci using data from all available genome-wide association studies. METHODS AND RESULTS: Through a meta-analysis of 6 genome-wide association study data sets and a validation study totaling 10 204 cases and 107 766 controls, we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches, we observed no new associations between the lead AAA single nucleotide polymorphisms and coronary artery disease, blood pressure, lipids, or diabetes mellitus. Network analyses identified ERG, IL6R, and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9. CONCLUSIONS: The 4 new risk loci for AAA seem to be specific for AAA compared with other cardiovascular diseases and related traits suggesting that traditional cardiovascular risk factor management may only have limited value in preventing the progression of aneurysmal disease

Abdominal Aortic Aneurysm Is Associated with a Variant in Low-Density Lipoprotein Receptor-Related Protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10−5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10−5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10−10, odds ratio 1.15 [1.10–1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04–1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression