Biodegradation and Abiotic Degradation of Trifluralin: A Commonly Used Herbicide with a Poorly Understood Environmental Fate.

Trifluralin is a widely used dinitroaniline herbicide, which can persist in the environment and has substantial ecotoxicity, especially to aquatic organisms. Trifluralin is very insoluble in water (0.22 mg/L at 20 °C) and highly volatile (vapor pressure of 6.7 mPa at 20 °C); these physicochemical properties determine a large part of its environmental fate, which includes rapid loss from soils if surface-applied, strong binding to soil organic matter, and negligible leaching into water. The trifluralin structure contains a tertiary amino group, two nitro-groups and a trifluoromethyl- group. Despite the strongly xenobiotic character of some of these substituents, biodegradation of trifluralin does occur, and pure cultures of bacteria and fungi capable of partially degrading the molecule either by dealkylation or nitro-group reduction have been identified. There are many unanswered questions about the environmental fate and metabolism of this herbicide; the genes and enzymes responsible for biodegradation are largely unknown, the relative roles of abiotic processes vs growth-linked biodegradation vs cometabolism are unresolved, and the impact of different environmental factors on the rates and extents of biodegradation are not clear. Here, we summarize the relevant literature on the persistence and environmental fate of trifluralin with a focus on biodegradation pathways and mechanisms, and we identify the current major knowledge gaps for future research.

Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa.

The gene RPGR was previously identified in the RP3 region of Xp21.1 and shown to be mutated in 10-20% of patients with the progressive retinal degeneration X-linked retinitis pigmentosa (XLRP). The mutations predominantly affected a domain homologous to RCC1, a guanine nucleotide exchange factor for the small GTPase Ran, although they were present in fewer than the 70-75% of XLRP patients predicted from linkage studies. Mutations in the RP2 locus at Xp11.3 were found in a further 10-20% of XLRP patients, as predicted from linkage studies. Because the mutations in the remainder of the XLRP patients may reside in undiscovered exons of RPGR, we sequenced a 172-kb region containing the entire gene. Analysis of the sequence disclosed a new 3' terminal exon that was mutated in 60% of XLRP patients examined. This exon encodes 567 amino acids, with a repetitive domain rich in glutamic acid residues. The sequence is conserved in the mouse, bovine and Fugu rubripes genes. It is preferentially expressed in mouse and bovine retina, further supporting its importance for retinal function. Our results suggest that mutations in RPGR are the only cause of RP3 type XLRP and account for the disease in over 70% of XLRP patients and an estimated 11% of all retinitis pigmentosa patients.

Constraining the response of continental-scale groundwater flow to climate change.

Numerical models of groundwater flow play a critical role for water management scenarios under climate extremes. Large-scale models play a key role in determining long range flow pathways from continental interiors to the oceans, yet struggle to simulate the local flow patterns offered by small-scale models. We have developed a highly scalable numerical framework to model continental groundwater flow which capture the intricate flow pathways between deep aquifers and the near-surface. The coupled thermal-hydraulic basin structure is inferred from hydraulic head measurements, recharge estimates from geochemical proxies, and borehole temperature data using a Bayesian framework. We use it to model the deep groundwater flow beneath the Sydney-Gunnedah-Bowen Basin, part of Australia's largest aquifer system. Coastal aquifers have flow rates of up to 0.3 m/day, and a corresponding groundwater residence time of just 2,000 years. In contrast, our model predicts slow flow rates of 0.005 m/day for inland aquifers, resulting in a groundwater residence time of [Formula: see text] 400,000 years. Perturbing the model to account for a drop in borehole water levels since 2000, we find that lengthened inland flow pathways depart significantly from pre-2000 streamlines as groundwater is drawn further from recharge zones in a drying climate. Our results illustrate that progressively increasing water extraction from inland aquifers may permanently alter long-range flow pathways. Our open-source modelling approach can be extended to any basin and may help inform policies on the sustainable management of groundwater.

Space-time modelling of groundwater level and salinity.

Soil salinization resulting from shallow saline groundwater is a major global environmental issue causing land degradation, especially in semi-arid regions such as Australia. The adverse impact of shallow saline groundwater on soil salinization varies in space and time due to the variation in groundwater levels and salt concentration. Understanding the spatio-temporal variation is therefore vital to develop an effective salinity management strategy. In New South Wales, Australia, a hydrogeological landscape unit approach is generally applied, based on spatial information and expert operators, classifying the landscape in relation to landscape and climate. In this paper, a data science approach (random forest model) is introduced, based on historical groundwater quality and quantity data providing predictions in a 4-dimensional space. As a case study, we demonstrate the spatio-temporal factors impacting standing water levels (SWL) and associated salinity and predict the spatial and temporal variability in the Muttama catchment (1059 km2), in NSW, south eastern Australia. The random forest model explains 77% of the variance in the groundwater salinity (electrical conductivity) and 65% of the SWL. Spatial factors were the most significant variables determining the space-time variation in groundwater salinity and the occurrence of groundwater at the surface. Drilled piezometer depth and elevation are dominant factors controlling SWL, while salinity is mainly determined by underlying geology. The methodology in this study predicts salinity and SWL in the landscape at fine scales, through time, improving options for salinity management.

Reduction of particulate matter concentrations by local removal in a building courtyard: Case study for the Delhi American Embassy School.

Exposure to particulate matter (PM) is strongly linked to human morbidity and mortality, where higher exposure entails higher all-cause daily mortality and increased long-term risk of cardiopulmonary mortality. The objective of this study is to demonstrate how and to what extent the local removal of PM2.5 can lead to reduced exposure for the children and teachers in the naturally ventilated courtyard of the American Embassy School (AES) high school building in Delhi. The study is performed by computational fluid dynamics (CFD) with the 3D steady Reynolds-averaged Navier-Stokes (RANS) equations in combination with the realizable k-ε turbulence model on a very high resolution grid. First, CFD validation is performed using wind-tunnel experiments of the flow pattern in and above a generic single street canyon. Next, the case study is conducted where four commercially available electrostatic precipitation (ESP) units are installed at different positions inside the courtyard and the resulting performance is evaluated. PM2.5 dispersion is modeled with an Eulerian advection-diffusion equation. It is shown that the best ESP positions yield overall volume-averaged PM2.5 concentration reductions up to 34.1% in the courtyard's corridors, demonstrating the proposed mitigation strategy to be effective. Perspectives for further reduction of the PM concentrations and the related reduction of health risks are discussed.

Detecting the impact of land cover change on observed rainfall.

Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002-2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region.

Microcosm experiments and kinetic modeling of glyphosate biodegradation in soils and sediments.

Glyphosate (GLP) is one of the most widely-used herbicides globally and its toxicity to humans and the environment is controversial. GLP is biodegradable, but little is known about the importance of site exposure history and other environmental variables on the rate and pathway of biodegradation. Here, GLP was added to microcosms of soils and sediments with different exposure histories and these were incubated with amendments of glucose, ammonium, and phosphate. GLP concentrations were measured with a newly-developed HPLC method capable of tolerating high concentrations of ammonium and amino acids. GLP biodegradation occurred after a lag-time proportional to the level of GLP pre-exposure in anthropogenically-impacted samples (soils and sediments), while no degradation occurred in samples from a pristine sediment after 180 days of incubation. Exposure history did not influence the rate of GLP degradation, after the lag-time was elapsed. Addition of C, N, and P triggered GLP degradation in pristine sediment and shortened the lag-time before degradation in other samples. In all microcosms, GLP was metabolised into aminomethylphosphonic acid (AMPA), which was highly persistent, and thus appears to be a more problematic pollutant than GLP. Bacterial communities changed along the gradients of anthropogenic impacts, but in some cases, taxonomically very-similar communities showed dramatically different activities with GLP. Our findings reveal important interactions between agriculturally-relevant nutrients and herbicides.

Can a growth model be used to describe forest carbon and water balance after fuel reduction burning in temperate forests?

Empirical evidence from Australia shows that fuel reduction burning significantly reduces the incidence and extent of unplanned fires. However, the integration of environmental values into fire management operations is not yet well-defined and requires further research and development. WAVES, a plant growth model that incorporates Soil-Vegetation-Atmosphere Transfer, was used to simulate the hydrological and ecological effects of three fuel management scenarios on a forest ecosystem. WAVES was applied using inputs from a set of forest plots for one year after three potential scenarios: (1) all litter removed, (2) all litter and 50% of the understorey removed, (3) all litter and understorey removed. Modelled outputs were compared with sites modelled with no-fuel reduction treatment (Unburnt). The key change between unburnt and fuel reduced forests was a significant increase in soil moisture after fire. Predictions of the recovery of aboveground carbon as plant biomass were driven by model structure and thus variability in available light and soil moisture at a local scale. Similarly, effects of fuel reduction burning on water processes were mainly due to changes in vegetation interception capacity (i.e. regrowth) and soil evaporation. Predicted effects of fuel reduction burning on total evapotranspiration (ET) - the major component of water balance - were marginal and not significant, even though a considerable proportion of ET had effectively been transferred from understorey to overstorey. In common with many plant growth models, outputs from WAVES are dictated by the assumption that overstorey trees continue to grow irrespective of their age or stage of maturity. Large areas of eucalypt forests and woodlands in SE Australia are well beyond their aggrading phase and are instead over-mature. The ability of these forests to rapidly respond to greater availability of water remains uncertain.

Glyphosate dispersion, degradation, and aquifer contamination in vineyards and wheat fields in the Po Valley, Italy.

Biodegradation of glyphosate (GLP) and its metabolite aminomethylphosphonic acid (AMPA) was numerically assessed for a vineyard and a wheat field in the Po Valley, Italy. Calculation of the Hazard Quotient suggested that GLP and AMPA can pose a risk of aquifer contamination in the top 1.5 m depth within 50 years of GLP use. Numerical results relative to soil GLP and AMPA concentrations, and GLP age, half life, and turnover time show that GLP was equivalently removed through hydrolysis and oxidation, but the latter produced AMPA. Biodegradation processes in the root zone removed more than 90% of applied GLP and more than 23% of the produced AMPA between two consecutive applications. Doubling organic carbon availability enhanced GLP and AMPA biodegradation, especially GLP hydrolysis to sarcosine. This work highlights that GLP and AMPA removal is controlled by soil water dynamics that depend on ecohydrological boundary conditions, and by carbon sources availability to biodegraders.

Vegetation and terrain drivers of infiltration depth along a semiarid hillslope.

An improved understanding of the drivers controlling infiltration patterns in semiarid regions is of key importance, as they have important implications for ecosystem productivity, retention of resources and the restoration of degraded areas. The infiltration depth variability (ΔInf) in vegetation patches at the hillslope scale can be driven by different factors along the hillslope. Here we investigate the effects of vegetation and terrain attributes under hypothesis that these attributes exert a major control in ΔInf within the patches. We characterise the ΔInf within vegetation patches at a semiarid hillslope located at the Jornada Experimental Range at dry antecedent conditions preceding two winter frontal rainfall events. We measured these events that are typical during winter conditions, and are characterised by low intensity (0.67 and 4.48 mm h-1) and a total rainfall of 10.4 and 4.6 mm. High precision geo-referenced wetting front depth measurements were taken at various locations within the vegetation patches using differential GPS. Vegetation and terrain attributes were analysed to explain the ΔInf among the vegetation patches. The infiltration depths in the periphery of the patches were in general considerably deeper than those in the centre. The observations suggest that the upslope margin of the patches received additional water in the form of runon from upslope adjacent bare soil. Patch orientation with regard to the slope dictated the effect of the rest of the patch attributes and the distance to the hillslope crest on ΔInf. We found that primarily patch orientation, followed by shape and size modulate lateral surface water transport through their effects on overland flow paths and water retention; something that would be obscured under more simplistic characterisations based on bare versus uniform vegetated soil discrimination.

Three novel mutations of the RPGR gene exon ORF15 in three Japanese families with X-linked retinitis pigmentosa.

We describe three new mutations in a recently identified exon, ORF15, of the retinitis pigmentosa GTPase regulator gene (RPGR) in three unrelated Japanese families (Families 1-3) with X-linked retinitis pigmentosa (XLRP). The affected males had typical retinitis pigmentosa (RP), whereas the obligate carrier females showed a wide clinical spectrum, ranging from minor symptoms to severe visual disability. Some carrier females in Families 1 and 2 showed typical RP, most carriers manifested high myopia and astigmatism, and their corrected visual acuity was insufficient. They showed an impairment of cone function following the rod dysfunction and accompanied by refractive errors. Microsatellite analysis of Family 1 revealed that the RP in the family was linked to the RP3 locus. Although one patient in the family had no mutation in the previously published exons 1-19 including exon 15a, he had a single-nucleotide insertion in exon ORF15 (g.ORF15 + 753-754 insG). Likewise, patients in Families 2 and 3 had two-base insertion/deletion in the exon, i.e., g.ORF15 + 833-834delGG and g.ORF15 + 861-862insGG, respectively. These insertional/deletional mutations observed in the three families are all different and new, and are predicted to lead to a frameshift, resulting in a truncated protein. These findings may support the previous hypothesis that RPGR-ORF15 is a mutational hot spot.

Characterisation of reversed-phase stationary phases for the liquid chromatographic analysis of basic pharmaceuticals by thermodynamic data.

This paper describes the characterisation of reversed-phase liquid chromatography (RPLC) columns using thermodynamic measurements. Retention versus 1/T data were used to construct Van't Hoff plots. The slope of these plots indicates the standard enthalpy of transfer of the analyte from the mobile to the stationary phase. The standard entropy can be calculated from the intercept. Van't Hoff plots were linear for the investigated RPLC columns, meaning that for basic analytes over the temperature range studied no changes in the retention mechanism occurred. Enthalpies and entropies of transfer of basic analytes from the mobile to the stationary phase revealed information about the types of interaction of protonated and neutral compounds with the stationary phases. However, a clear view using the present set of basic compounds on how these thermodynamic data may explain the observed substantial differences in peak symmetry cannot be given. It is considered that addition of N,N-dimethyloctylamine (DMOA) to the eluent will results in a dynamically coating of the stationary phase. Addition of DMOA to the eluent resulted for protonated basic compounds in a reduction of both enthalpy and entropy. In practice, with DMOA in the eluent symmetrical peaks were obtained. It is assumed that this is due to blocking residual silanols and/or ion exclusion effects.

Characterisation of reversed-phase liquid chromatography stationary phases for the analysis of basic pharmaceuticals: eluent properties and comparison of empirical test methods.

The reversed-phase liquid chromatographic analysis of basic pharmaceuticals can be problematic. Both the properties of the eluent and the stationary phase can influence the chromatographic performance. Therefore selection of suitable experimental conditions for the analysis of basic compounds can be difficult. This paper shows that the organic modifier and the nature of the buffer influence the eluent properties. Moreover, the nature and amount of modifier also influence the basicity of the analytes. Investigations showed that the nature of the buffer can have a significant influence on retention and peak shape of basic compounds. Test procedures using basic analytes as test probes provided relevant information with respect to selecting columns to analyse basic pharmaceutical compounds. Test procedures using compounds like aniline, phenol and benzene were found to be less suitable.

Preliminary study on the effect of miniaturisation and use of volatile mobile phases in LC for the on-line LC-MS analysis of basic pharmaceuticals.

To enhance to compatibility of the on-line coupling of liquid chromatography (LC) with mass spectrometry (MS) for the analysis of basic pharmaceuticals, the use of volatile mobile phase systems in combination with miniaturised LC was investigated. Multifactor analysis of variance (MANOVA) was used to evaluate the data obtained for the various variables (modifier, stationary phase, buffer, buffer pH and buffer concentration) on the resolution, peak symmetry and retention of four basic compounds analysed using LC columns with internal diameters (I.D.) of 0.3, 1.0 and 4.6 mm (conventional). Preliminary results obtained with the investigated micro and conventional columns showed similar behaviour with respect to ruggedness. The various investigated variables showed that miniaturisation by simply downscaling dimensions can result in varying selectivity and peak shapes for basic compounds. When comparing volatile mobile phases (containing ammonium acetate or ammonium citrate) and a conventional non-volatile mobile phase (containing sodium phosphate) under pH 3 conditions, similar separation performances were observed. In the present study, ammonium citrate as the buffering salt, a high buffer concentration and methanol as the modifier showed the best peak symmetry.

Near surface water balance in the Northern Murray-Darling Basin.

The water balance allows the calculation of deep drainage from other components of the hydrological cycle. Deep drainage has been linked to outbreaks of dryland and irrigated salinity. Until recently, deep drainage was not considered to be an issue on the alluvial plains of the Northern Murray-Darling Basin. Recent simulation studies and calculations using the water balance suggest that substantial deep drainage occurs under irrigated agriculture. However, these estimates have large uncertainties due to possible errors in measurement, calculation and due to spatial variability. On a catchment scale the relative area under a certain land use as well as the connection to local groundwater and the influence of anomalies such as prior streams needs to be considered. This paper discusses the current state of knowledge on the water balance in the Northern Murray-Darling Basin and highlights the need for a concentrated effort to measure all the components of the water balance in this area, as well as the effect on shallow groundwater quality and levels.

RPGR ORF15 isoform co-localizes with RPGRIP1 at centrioles and basal bodies and interacts with nucleophosmin.

The ORF15 isoform of RPGR (RPGR(ORF15)) and RPGR interacting protein 1 (RPGRIP1) are mutated in a variety of retinal dystrophies but their functions are poorly understood. Here, we show that in cultured mammalian cells both RPGR(ORF15) and RPGRIP1 localize to centrioles. These localizations are resistant to the microtubule destabilizing drug nocodazole and persist throughout the cell cycle. RPGR and RPGRIP1 also co-localize at basal bodies in cells with primary cilia. The C-terminal (C2) domain of RPGR(ORF15) (ORF15(C2)) is highly conserved across 13 mammalian species, suggesting that it is a functionally important domain. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we show that this domain interacts with a 40 kDa shuttling protein nucleophosmin (NPM). The RPGR(ORF15)-NPM interaction was confirmed by (i) yeast two-hybrid analyses; (ii) binding of both recombinant and native HeLa cell NPM to RPGR(ORF15) fusion proteins in vitro; (iii) co-immunoprecipitation of native NPM, RPGR(ORF15) and RPGRIP1 from bovine retinal extracts and of native HeLa cell NPM and transfected RPGR(ORF15) from cultured cells and (iv) co-localization of NPM and RPGR(ORF15) at metaphase centrosomes in cultured cells. NPM is a multifunctional protein chaperone that shuttles between the nucleoli and the cytoplasm and has been associated with licensing of centrosomal division. RPGR and RPGRIP1 join a growing number of centrosomal proteins involved in human disease.

Molecular analysis of a patient with hydrops fetalis caused by beta-glucuronidase deficiency, and evidence for additional pseudogenes.

A patient with hydrops fetalis caused by beta-glucuronidase deficiency was found to be homozygous for a C to T transition at nucleotide position 672 in his cDNA. Genomic analysis showed the presence of pseudogenes for the beta-glucuronidase gene. After separation of PCR products of the gene and the pseudogenes it was shown that the patient and his father were heterozygous for the C-T 672 transition and the mother did not carry the mutation.

A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human beta-glucuronidase gene.

We have previously sequenced the complete coding region and the promoter region of the beta-glucuronidase gene of a patient with mild mucopolysaccharidosis type VII (MPS VII) and identified a nonsense mutation in the gene inherited from her mother. The mutation inherited from her father was not found. Here, we have extended the sequence analysis of the introns to cover all putative lariat branch points and putative intronic enhancers, although no nucleotide changes have been found in these regions. Careful analysis of mRNA structure by reverse transcription/polymerase chain reaction (RT-PCR) and direct sequencing has revealed the inclusion of a new exon derived from an antisense Alu-repeat in intron 8 and the skipping of exon 9 in a large proportion of the mRNA of our patient. A 2-bp deletion creating a strong 5'-splice site has subsequently been identified in the paternal gene of the patient (IVS8+0.6kbdelTC). With a sensitive RT-PCR assay, we demonstrate that both the inclusion of the Alu-cassette and the skipping of exon 9 are minor events in control samples and that mRNA with both alterations is only found in the IVS8+0.6kbdelTC carrier. The increased proportion of exon 9 skipping seems to be related to the premature termination of translation. This is the third report of a human disease mutation that creates a splice site and activates an antisense Alu-cassette; the question rises as to how these apparently strong cryptic exons are generally excluded from coding sequences.

Antithrombin-Gly 424 Arg: a novel point mutation responsible for type 1 antithrombin deficiency and neonatal thrombosis.

Inherited type 1 antithrombin (AT) III deficiency is characterized by a decrease of immunoreactive and functional protein levels to about 50%. The disorder is associated with a significantly increased risk of thromboembolism. We have investigated the molecular basis of type 1 AT deficiency in a Belgian family. The diagnosis of the disease was primarily made in a newborn girl with unusually severe thrombotic complications. Using the polymerase chain reaction and single-strand conformation polymorphism analysis, followed by direct sequencing of AT gene fragments, we identified a novel point mutation in exon 6. We detected a G to C substitution in the first position of codon 424 leading to a glycine to arginine substitution. The modification at this highly conserved position in the serine protease inhibitor gene family probably leads to an unstable mutant-gene product. The mutation creates a unique restriction site for the enzyme Hha I in exon 6. This change permitted a rapid and accurate screening of the kindred with identification of the molecular defect in five other family members.

Localization by fluorescence in situ hybridization of the human functional beta-glucuronidase gene (GUSB) to 7q11.21 --> q11.22 and two pseudogenes to 5p13 and 5q13.

The gene coding for human beta-glucuronidase (GUSB) was mapped to 7q11.21 --> q11.22 by fluorescence in situ hybridization (FISH), thus clarifying the contradictory published localizations of this gene. Multiple unprocessed pseudogenes and pseudogene fragments for GUSB have been described. However, only two weak signals, one at chromosome band 5p13 and the other at 5q13, could be detected with FISH, suggesting considerable divergence between GUSB and its related sequences.