The cost-effectiveness of germline BRCA testing in metastatic prostate cancer followed by cascade testing of first-degree relatives of mutation carriers.

OBJECTIVES: Metastatic prostate cancer (mPCa) patients with BRCA mutations benefit from targeted treatments (e.g., olaparib). Additionally, family members of affected patients have increased risk of hereditary cancers and benefit from early detection and prevention. International guidelines recommend genetic testing in mPCa, however, the value for money of testing mPCa patients and cascade testing of blood-related family members has not been assessed. In this context we evaluated the cost-effectiveness of germline BRCA testing in mPCa patients followed by cascade testing of first-degree relatives (FDRs) of mutation carriers. METHODS: We conducted a cost-utility analysis of germline BRCA testing using two scenarios: 1) testing mPCa patients only; 2) testing mPCa patients and first-degree relatives (FDRs) of those who test positive. A semi-Markov multi-health-state transition model was constructed using a lifetime time horizon. The analyses were performed from an Australian payer perspective. Decision uncertainty was characterized using probabilistic analyses. RESULTS: Compared with no testing, BRCA testing in mPCa was associated with an incremental cost of AU$3,731 and a gain of 0.014 quality-adjusted life years (QALYs), resulting in an incremental cost-effectiveness ratio (ICER) of AU$265,942/QALY. Extending testing to FDRs of variant positive patients resulted in an ICER of AU$16,392/QALY. Probability of cost-effectiveness at a willingness-to-pay of AU$75,000/QALY was 0% in the standalone mPCa analysis and 100% in the cascade testing analysis. CONCLUSION: BRCA testing when performed as a standalone strategy in patients with mPCa may not be cost-effective but demonstrates significant value for money after the inclusion of cascade testing of FDRs of mutation carriers.

Whole Genome Sequencing in Advanced Lung Cancer can be Performed Using Diff-Quik Cytology Smears Derived from Endobronchial Ultrasound, Transbronchial Needle Aspiration (EBUS TBNA).

INTRODUCTION: Maximising alternative sample types for genomics in advanced lung cancer is important because bronchoscopic samples may sometimes be insufficient for this purpose. Further, the clinical applications of comprehensive molecular analysis such as whole genome sequencing (WGS) are rapidly developing. Diff-Quik cytology smears from EBUS TBNA is an alternative source of DNA, but its feasibility for WGS has not been previously demonstrated. METHODS: Diff-Quik smears were collected along with research cell pellets. RESULTS: Tumour content of smears were compared to research cell pellets from 42 patients, which showed good correlation (Spearman correlation 0.85, P < 0.0001). A subset of eight smears underwent WGS, which presented similar mutation profiles to WGS of the matched cell pellet. DNA yield was predicted using a regression equation of the smears cytology features, which correctly predicted DNA yield > 1500 ng in 7 out of 8 smears. CONCLUSIONS: WGS of commonly collected Diff-Quik slides is feasible and their DNA yield can be predicted.

A Combined Quantitative Evaluation Model for the Capability of Hyperspectral Imagery for Mineral Mapping.

To analyze the influence factors of hyperspectral remote sensing data processing, and quantitatively evaluate the application capability of hyperspectral data, a combined evaluation model based on the physical process of imaging and statistical analysis was proposed. The normalized average distance between different classes of ground cover is selected as the evaluation index. The proposed model considers the influence factors of the full radiation transmission process and processing algorithms. First- and second-order statistical characteristics (mean and covariance) were applied to calculate the changes for the imaging process based on the radiation energy transfer. The statistical analysis was combined with the remote sensing process and the application performance, which consists of the imaging system parameters and imaging conditions, by building the imaging system and processing models. The season (solar zenith angle), sensor parameters (ground sampling distance, modulation transfer function, spectral resolution, spectral response function, and signal to noise ratio), and number of features were considered in order to analyze the influence factors of the application capability level. Simulated and real data collected by Hymap in the Dongtianshan area (Xinjiang Province, China), were used to estimate the proposed model's performance in the application of mineral mapping. The predicted application capability of the proposed model is consistent with the theoretical analysis.

Contaminants of Emerging Concern: Mass Balance and Comparison of Wastewater Effluent and Upstream Sources in a Mixed-Use Watershed.

Understanding the sources, transport, and spatiotemporal variability of contaminants of emerging concern (CECs) is important for understanding risks and developing monitoring and mitigation strategies. This study used mass balances to compare wastewater treatment plant (WWTP) and upstream sources of 16 CECs to a mixed-use watershed in Minnesota, under different seasonal and hydrological conditions. Three distinct CEC groups emerged with respect to their source proportionality and instream behavior. Agricultural herbicides and daidzein inputs were primarily via upstream routes with the greatest loadings and concentrations during high flows. Trimethoprim, mecoprop, nonprescription pharmaceuticals, and personal care products entered the system via balanced/mixed pathways with peak loadings and concentrations in high flows. Carbaryl, 4-nonylphenol, and the remaining prescription pharmaceuticals entered the system via WWTP effluent with relatively stable loadings across sampling events. Mass balance analysis based on multiple sampling events and sites facilitated CEC source comparisons and may therefore prove to be a powerful tool for apportioning sources and exploring mitigation strategies.

Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing.

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.

Iron-enhanced sand filters: Multi-year urban runoff (stormwater) quality performance.

Untreated urban runoff (stormwater) is a major pathway for contaminants, e.g., nutrients and metals, to receiving waters. Where eutrophication occurs, dissolved phosphorus (DP) treatment is often necessary to protect receiving waters, yet few practical methods exist. Iron-enhanced sand filters (IESFs) have successfully treated DP in laboratory and limited field studies. Yet, multi-year-IESF studies to understand reportedly variable performance are unavailable. Herein, nine IESFs were sampled from 2015 to 2018 (528 samples; 70 rainfall-runoff events). Analysis focused on influent/effluent concentrations and removal efficiencies alongside design and catchment parameters. Overall, IESFs significantly removed most total and dissolved metal analytes. Generally, phosphorus removal efficiencies correlated positively with influent concentrations and IESF:catchment area ratios, demonstrating the importance of proper sizing and siting. For all paired influent-effluent samples, respective median total phosphorus, orthophosphate, and DP removal efficiencies were 33 %, 41 %, and 13 %, and respective median effluent concentrations were 120, 25, and 75 (µg/L); with two malfunctioning sites omitted, these respective concentrations were 92, 11, and 47, which better matched relevant goals and (indirectly applicable) standards. Nonetheless, phosphorus removal efficiency and effluent concentrations varied significantly across IESFs and events. Seasonality appeared influential, yet variable influent concentrations confounded spatiotemporal removal efficiency comparisons. Thus, compared to removal efficiencies, effluent concentrations may be better indicators of receiving water risk/benefit and of equal importance for water quality crediting. Although 122 influent-effluent pairs were analyzed, a greater sample size would allow multivariate hypothesis tests with additional predictors. Overall, in this multi-site-year study, most IESFs performed at (n = 5) or near (n = 2) phosphorus effluent concentration and less-so, removal efficiency benchmarks. This research provides new quantitative knowledge on long-term IESF performance for real-world conditions and goals. Research recommendations include multivariate dimension reduction studies and comprehensive, effective information transfer to improve IESF understanding and performance and address practitioner needs, e.g., for refined design, operation, and assessment guidance.

Guidelines for genetic testing in prostate cancer: a scoping review.

BACKGROUND: Genetic testing, to identify pathogenic or likely pathogenic variants in prostate cancer, is valuable in guiding treatment decisions for men with prostate cancer and to inform cancer prevention and early detection options for their immediate blood relatives. There are various guidelines and consensus statements for genetic testing in prostate cancer. Our aim is to review genetic testing recommendations across current guidelines and consensus statements and the level of evidence supporting those recommendations. METHODS: A scoping review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for scoping review (PRISMA-ScR) guidelines. Electronic database searches and manual searches of grey literature, including websites of key organisations were conducted. Using the Population, Concept, Context (PCC) framework, this scoping review included: men with prostate cancer or men at high risk of prostate cancer and their biological families; existing guidelines and consensus statements with supporting evidence for genetic testing of men with prostate cancer from any geographical location worldwide. RESULTS: Of the 660 citations identified, 23 guidelines and consensus statements met the inclusion criteria for the scoping review. Based on different levels of evidence about who should be tested and how, a diverse range of recommendations were identified. There was general consensus among the guidelines and consensus statements that men with metastatic disease be offered genetic testing; however, there was less consensus in relation to genetic testing in localised prostate cancer. While there was some consensus in relation to which genes to test, recommendations varied regarding who to test, testing methods and implementation. CONCLUSION: While genetic testing in prostate cancer is routinely recommended and numerous guidelines exist, there is still considerable lack of consensus regarding who should be tested and how they should be tested. Further evidence is needed to inform value-based genetic testing strategies for implementation in practice.

Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples.

BACKGROUND: Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels. METHODS: A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina). RESULTS: Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden. CONCLUSIONS: Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.

Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report.

Introduction: Tumour Mutation Burden (TMB) is a potential biomarker for immune cancer therapies. Here we investigated parameters that might affect TMB using duplicate cytology smears obtained from endobronchial ultrasound transbronchial needle aspiration (EBUS TBNA)-sampled malignant lymph nodes. Methods: Individual Diff-Quik cytology smears were prepared for each needle pass. DNA extracted from each smear underwent sequencing using large gene panel (TruSight Oncology 500 (TSO500 - Illumina)). TMB was estimated using the TSO500 Local App v. 2.0 (Illumina). Results: Twenty patients had two or more Diff-Quik smears (total 45 smears) which passed sequencing quality control. Average smear TMB was 8.7 ± 5.0 mutations per megabase (Mb). Sixteen of the 20 patients had paired samples with minimal differences in TMB score (average difference 1.3 ± 0.85). Paired samples from 13 patients had concordant TMB (scores below or above a threshold of 10 mutations/Mb). Markedly discrepant TMB was observed in four cases, with an average difference of 11.3 ± 2.7 mutations/Mb. Factors affecting TMB calling included sample tumour content, the amount of DNA used in sequencing, and bone fide heterogeneity of node tumour between paired samples. Conclusion: TMB assessment is feasible from EBUS-TBNA smears from a single needle pass. Repeated samples of a lymph node station have minimal variation in TMB in most cases. However, this novel data shows how tumour content and minor change in site of node sampling can impact TMB. Further study is needed on whether all node aspirates should be combined in 1 sample, or whether testing independent nodes using smears is needed.

Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies.

A major challenge in ecotoxicology is accurately and sufficiently measuring chemical exposures and biological effects given the presence of complex and dynamic contaminant mixtures in surface waters. It is impractical to quantify all chemicals in such matrices over space and time, and even if it were practical, concomitant biological effects would not be elucidated. Our study examined the performance of the Daphnia magna transcriptome to detect distinct responses across three water sources in Minnesota: laboratory (well) waters, wetland waters, and storm waters. Pyriproxyfen was included as a gene expression and male neonate production positive control to examine whether gene expression resulting from exposure to this well-studied juvenoid hormone analog can be detected in complex matrices. Laboratory-reared (<24 h) D. magna were exposed to a water source and/or pyriproxyfen for 16 days to monitor phenotypic changes or 96 h to examine gene expression responses using Illumina HiSeq 2500 (10 million reads per library, 50-bp paired end [2 × 50]). The results indicated that a unique gene expression profile was produced for each water source. At 119 ng/L pyriproxyfen (~25% effect concentration) for male neonate production, as expected, the Doublesex1 gene was up-regulated. In descending order, gene expression patterns were most discernable with respect to pyriproxyfen exposure status, season of stormwater sample collection, and wetland quality, as indicated by the index of biological integrity. However, the biological implications of the affected genes were not broadly clear given limited genome resources for invertebrates. Our study provides support for the utility of short-term whole-organism transcriptomic testing in D. magna to discern sample type, but highlights the need for further work on invertebrate genomics. Environ Toxicol Chem 2022;41:2107-2123. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Contaminants of emerging concern in urban stormwater: Spatiotemporal patterns and removal by iron-enhanced sand filters (IESFs).

Numerous contaminants of emerging concern (CECs) typically occur in urban rivers. Wastewater effluents are a major source of many CECs. Urban runoff (stormwater) is a major urban water budget component and may constitute another major CEC pathway. Yet, stormwater-based CEC field studies are rare. This research investigated 384 CECs in 36 stormwater samples in Minneapolis-St. Paul, Minnesota, USA. Nine sampling sites included three large stormwater conveyances (pipes) and three paired iron-enhanced sand filters (IESFs; untreated inlets and treated outlets). The 123 detected compounds included commercial-consumer compounds, veterinary and human pharmaceuticals, lifestyle and personal care compounds, pesticides, and others. Thirty-one CECs were detected in ≥50% of samples. Individual samples contained a median of 35 targeted CECs (range: 18-54). Overall, median concentrations were ≥10 ng/L for 25 CECs and ≥100 ng/L for 9 CECs. Ranked, hierarchical linear modeling indicated significant seasonal- and site type-based concentration variability for 53 and 30 CECs, respectively, with observed patterns corresponding to CEC type, source, usage, and seasonal hydrology. A primarily warm-weather, diffuse, runoff-based profile included many herbicides. A second profile encompassed winter and/or late summer samples enriched with some recalcitrant, hydrophobic compounds (e.g., PAHs), especially at pipes, suggesting conservative, less runoff-dependent sources (e.g., sediments). A third profile, indicative of mixed conservative/non-runoff, runoff, and/or atmospheric sources and transport that collectively affect a variety of conditions, included various fungicides, lifestyle, non-prescription, and commercial-consumer CECs. Generally, pipe sites had large, diverse land-use catchments, and showed more frequent detections of diverse CECs, but often at lower concentrations; while untreated sites (with smaller, more residential-catchments) demonstrated greater detections of "pseudo-persistent" and other ubiquitous or residentially-associated CECs. Although untreated stormwater transports an array of CECs to receiving waters, IESF treatment significantly removed concentrations of 14 (29%) of the 48 most detected CECs; for these, median removal efficiencies were 26%-100%. Efficient removal of some hydrophobic (e.g., PAHs, bisphenol A) and polar-hydrophilic (e.g., caffeine, nicotine) compounds indicated particulate-bound contaminant filtration and for certain dissolved contaminants, sorption.

Effects of urban stormwater and iron-enhanced sand filtration on Daphnia magna and Pimephales promelas.

Urban stormwater is an important but incompletely characterized contributor to surface-water toxicity. The present study used 5 bioassays of 2 model organisms (Daphnia magna and fathead minnow, Pimephales promelas) to investigate stormwater toxicity and mitigation by full-scale iron-enhanced sand filters (IESFs). Stormwater samples were collected from major stormwater conveyances and full-scale IESFs during 4 seasonal events (winter snowmelt and spring, early summer, and late summer rainfalls) and analyzed for a diverse range of contaminants of emerging concern including pharmaceuticals, personal care products, industrial chemicals, and pesticides. Concurrently, stormwater samples were collected for toxicity testing. Seasonality appeared more influential and consistent than site type for most bioassays. Typically, biological consequences were least in early summer and greatest in late summer and winter. In contrast with the unimproved and occasionally reduced biological outcomes in IESF-treated and late summer samples, water chemistry indicated that numbers and total concentrations of detected organic chemicals, metals, and nutrients were reduced in late summer and in IESF-treated stormwater samples. Some potent toxicants showed more specific seasonality (e.g., high concentrations of polycyclic aromatic hydrocarbons and industrial compounds in winter, pesticides in early summer and spring, flame retardants in late summer), which may have influenced outcomes. Potential explanations for insignificant or unexpected stormwater treatment outcomes include confounding effects of complex stormwater matrices, IESF nutrient removal, and, less likely, unmonitored toxicants. Environ Toxicol Chem 2018;37:2645-2659. © 2018 SETAC.

Demonstration of a novel Xp22.2 microdeletion as the cause of familial extreme skewing of X-inactivation utilizing case-parent trio SNP microarray analysis.

BACKGROUND: We report a kindred referred for molecular investigation of severe hemophilia A in a young female in which extremely skewed X-inactivation was observed in both the proband and her clinically normal mother. METHODS: Bidirectional Sanger sequencing of all F8 gene coding regions and exon/intron boundaries was undertaken. Methylation-sensitive restriction enzymes were utilized to investigate skewed X-inactivation using both a classical human androgen receptor (HUMARA) assay, and a novel method targeting differential methylation patterns in multiple informative X-chromosome SNPs. Illumina Whole-Genome Infinium microarray analysis was performed in the case-parent trio (proband and both parents), and the proband's maternal grandmother. RESULTS: The proband was a cytogenetically normal female with severe hemophilia A resulting from a heterozygous F8 pathogenic variant inherited from her similarly affected father. No F8 mutation was identified in the proband's mother, however, both the proband and her mother both demonstrated completely skewed X-chromosome inactivation (100%) in association with a previously unreported 2.3 Mb deletion at Xp22.2. At least three disease-associated genes (FANCB, AP1S2, and PIGA) were contained within the deleted region. CONCLUSIONS: We hypothesize that true "extreme" skewing of X-inactivation (≥95%) is a rare occurrence, but when defined correctly there is a high probability of finding an X-chromosome disease-causing variant or larger deletion resulting in X-inactivation through a survival disadvantage or cell lethal mechanism. We postulate that the 2.3 Mb Xp22.2 deletion identified in our kindred arose de novo in the proband's mother (on the grandfather's homolog), and produced extreme skewing of X-inactivation via a "cell lethal" mechanism. We introduce a novel multitarget approach for X-inactivation analysis using multiple informative differentially methylated SNPs, as an alternative to the classical single locus (HUMARA) method. We propose that for females with unexplained severe phenotypic expression of an X-linked recessive disorder trio-SNP microarray should be undertaken in combination with X-inactivation analysis.

Sources and transport of contaminants of emerging concern: A two-year study of occurrence and spatiotemporal variation in a mixed land use watershed.

The occurrence and spatiotemporal variation of 26 contaminants of emerging concern (CECs) were evaluated in 68 water samples in 2011-2012 in the Zumbro River watershed, Minnesota, U.S.A. Samples were collected across a range of seasonal/hydrological conditions from four stream sites that varied in associated land use and presence of an upstream wastewater treatment plant (WWTP). Selected CECs included human/veterinary pharmaceuticals, personal care products, pesticides, phytoestrogens, and commercial/industrial compounds. Detection frequencies and concentrations varied, with atrazine, metolachlor, acetaminophen, caffeine, DEET, and trimethoprim detected in more than 70% of samples, acetochlor, mecoprop, carbamazepine, and daidzein detected in 30%-50% of samples, and 4-nonylphenol, cotinine, sulfamethoxazole, erythromycin, tylosin, and carbaryl detected in 10%-30% of samples. The remaining target CECs were not detected in water samples. Three land use-associated trends were observed for the detected CECs. Carbamazepine, 4-nonylphenol, erythromycin, sulfamethoxazole, tylosin, and carbaryl profiles were WWTP-dominated, as demonstrated by more consistent loading and significantly greater concentrations downstream of the WWTP and during low-flow seasons. In contrast, acetaminophen, trimethoprim, DEET, caffeine, cotinine, and mecoprop patterns demonstrated both seasonally-variable non-WWTP-associated and continual WWTP-associated influences. Surface water studies of CECs often target areas near WWTPs. This study suggests that several CECs often characterized as effluent-associated have additional important sources such as septic systems or land-applied biosolids. Finally, agricultural herbicide (atrazine, acetochlor, and metolachlor) profiles were strongly influenced by agricultural land use and seasonal application-runoff, evident by significantly greater concentrations and loadings at upstream sites and in early summer when application and precipitation rates are greatest. Our results indicate that CEC monitoring studies should consider a range of land uses, seasonality, and transport pathways in relation to concentrations and loadings. This knowledge can augment CEC monitoring programs to result in more accurate source, occurrence, and ecological risk characterizations, more precisely targeted mitigation initiatives, and ultimately, enhanced environmental decision-making.

PineappleDB: an online pineapple bioinformatics resource.

BACKGROUND: A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. DESCRIPTION: PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. CONCLUSION: The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

Sediment-water distribution of contaminants of emerging concern in a mixed use watershed.

This study evaluated the occurrence and distribution of 15 contaminants of emerging concern (CECs) in stream water and sediments in the Zumbro River watershed in Minnesota and compared these with sub-watershed land uses. Sixty pairs of sediment and water samples were collected across all seasons from four stream sites for over two years and analyzed for selected personal care products, pesticides, human and veterinary medications, and phytoestrogens. Spatial and temporal analyses indicate that pharmaceuticals and personal care products (urban/residential CECs) are significantly elevated in water and/or sediment at sites with greater population density (>100 people/km(2)) and percentage of developed land use (>8% of subwatershed area) than those with less population density and land area under development. Significant spatial variations of agricultural pesticides in water and sediment were detectable, even though all sites had a high percentage of agricultural land use. Seasonality in CEC concentration was observed in water but not in sediment, although sediment concentrations of three CECs did vary between years. Average measured non-equilibrium distribution coefficients exceeded equilibrium hydrophobic partitioning-based predictions for 5 of the 7 detected CECs by at least an order of magnitude. Agreement of measured and predicted distribution coefficients improved with increasing hydrophobicity and in-stream persistence. The more polar and degradable CECs showed greater variability in measured distributions across different sampling events. Our results confirm that CECs are present in urban and agricultural stream sediments, including those CECs that would typically be thought of as non-sorptive based on their log Kow values. These results and the observed patterns of sediment and water distributions augment existing information to improve prediction of CEC fate and transport, leading to more accurate assessments of exposure and risk to surface water ecosystems.

Altered shoot/root Na+ distribution and bifurcating salt sensitivity in Arabidopsis by genetic disruption of the Na+ transporter AtHKT1.

Sodium (Na+) is toxic to most plants, but the molecular mechanisms of plant Na+ uptake and distribution remain largely unknown. Here we analyze Arabidopsis lines disrupted in the Na+ transporter AtHKT1. AtHKT1 is expressed in the root stele and leaf vasculature. athkt1 null plants exhibit lower root Na+ levels and are more salt resistant than wild-type in short-term root growth assays. In shoot tissues, however, athkt1 disruption produces higher Na+ levels, and athkt1 and athkt1/sos3 shoots are Na+-hypersensitive in long-term growth assays. Thus wild-type AtHKT1 controls root/shoot Na+ distribution and counteracts salt stress in leaves by reducing leaf Na+ accumulation.

Identifying sources of emerging organic contaminants in a mixed use watershed using principal components analysis.

Principal components analysis (PCA) was used to identify sources of emerging organic contaminants in the Zumbro River watershed in Southeastern Minnesota. Two main principal components (PCs) were identified, which together explained more than 50% of the variance in the data. Principal Component 1 (PC1) was attributed to urban wastewater-derived sources, including municipal wastewater and residential septic tank effluents, while Principal Component 2 (PC2) was attributed to agricultural sources. The variances of the concentrations of cotinine, DEET and the prescription drugs carbamazepine, erythromycin and sulfamethoxazole were best explained by PC1, while the variances of the concentrations of the agricultural pesticides atrazine, metolachlor and acetochlor were best explained by PC2. Mixed use compounds carbaryl, iprodione and daidzein did not specifically group with either PC1 or PC2. Furthermore, despite the fact that caffeine and acetaminophen have been historically associated with human use, they could not be attributed to a single dominant land use category (e.g., urban/residential or agricultural). Contributions from septic systems did not clarify the source for these two compounds, suggesting that additional sources, such as runoff from biosolid-amended soils, may exist. Based on these results, PCA may be a useful way to broadly categorize the sources of new and previously uncharacterized emerging contaminants or may help to clarify transport pathways in a given area. Acetaminophen and caffeine were not ideal markers for urban/residential contamination sources in the study area and may need to be reconsidered as such in other areas as well.