Mass spectral characterisation of cyclic oligoesters in a biodegradable mulch film.

RATIONALE: Plastic mulch film manages weed growth and moisture loss on the surface of cropping beds. The chemical components of such plastics include polymer(s), additives and non-intentionally added substances (NIASs). The unknown chemical nature and behaviours of these constituents require investigation due to their potential to add to the anthropogenic chemical burden in the agrifood system. METHODS: Solvent extracts of a commercial 15% polylactic acid (PLA)/85% poly(butylene adipate-co-terephthalate) mulch film were investigated using gas chromatography-mass spectrometry (GC-MS) with electron ionisation to characterise the additive and NIAS components. The obscurity of some of the NIASs meant their identification was not readily achieved through routine MS library comparisons. As such, the identification of several polymer-derived compounds required interpretation of the MS data and re-application of the derived fragmentation patterns with reference to the wider literature. Unknowns were confirmed using commercially available compounds. RESULTS: Unknown NIASs were identified as cyclic oligoesters comprised of the monomeric building blocks of the polymer system. Cyclic structures derived from the monomers of polybutylene adipate (PBA) and polybutylene terephthalate (PBT) fragmented through a primary pathway involving 1,5- and 1,3-H transfers at ester linkages. Characteristic ions at m/z 111, 129, 183 and 201 for PBA-derived cyclic oligoesters and m/z 104, 132, 149 and 221 for PBT-derived cyclic oligoesters were assigned in the mass spectra of unknowns. Cyclic oligoesters containing sebacate moieties were also identified, indicating the presence of polybutylene sebacate as an unexpected component of the mulch. CONCLUSIONS: Systematic analyses of the sort reported here are valuable for providing alternative approaches for the identification of plastic-related chemicals. Open publication of MS spectral data is required to build a greater understanding of the mulch film chemical components contributing to the environmental chemical load introduced to agroecosystems.

Patient Priorities in Autoimmune Hepatitis: The Need for Better Treatments, More Education and Challenging Stigma.

BACKGROUND: Data show that patients with autoimmune hepatitis have significantly reduced quality-of-life and that corticosteroids carry marked side effects. AIMS: This study explored patients' experiences of autoimmune hepatitis and its treatments; key aspects for developing safe and effective new approaches to therapy. METHODS: An anonymised, internet-based survey collected data including patient demographics, treatments, side-effects, impact on day-to-day life, sources of support and attitudes towards autoimmune hepatitis between December 2019-January 2020. Semi-structured interviews were conducted with 13 patients to further explore their support networks, treatment experiences and health priorities. Descriptive and quantitative analyses were undertaken using R and free text responses were subject to thematic analysis. RESULTS: In total, 270 survey responses were received (median age 55 years and 94% female). Perceived medication side-effects were reported by 66% (169/257) and 73% responded negatively about their experience of corticosteroids. The majority (62·3% [(109/175]) would 'definitely' or 'probably' consider clinical trial participation to improve their care. Only 18·7% (31/166) reported access to a specialist liver nurse and nearly half were involved in support groups. Interview and survey data suggested that major issues were stigma, loss of control and fatigue. CONCLUSIONS: This study provides insights into the realities of living with autoimmune hepatitis with clear issues around lack of support networks, need for patient empowerment and stigma surrounding liver disease. Patient priorities are better therapies to slow disease progression, avoiding corticosteroids and minimising side-effects. Patient willingness to participate in trials suggests that they are achievable provided they have the right design and clinical endpoints.

CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms.

DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been thoroughly explored. Here, we found that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1/3b undergo a partial epithelial to mesenchymal transition associated with increased CD44 variant exon skipping. These skipping events are directly mediated by the loss of intragenic meDNA and the chromatin factors MBD1/2/3 and HP1γ and are also linked to phosphorylation changes in elongating RNA polymerase II. The role of meDNA in alternative splicing was confirmed by using the dCas9/DNMT3b tool. We further tested whether the meDNA level could have predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes, mostly involved in splicing and signal transduction, are correlated with the local modulation of meDNA. Our observations suggest that, although DNA methylation has multiple avenues to affect alternative splicing, its indirect effect may also be mediated through alternative splicing isoforms of these meDNA sensors.

Untargeted characterisation of dissolved organic matter contributions to rivers from anthropogenic point sources using direct-infusion and high-performance liquid chromatography/Orbitrap mass spectrometry.

RATIONALE: Anthropogenic organic inputs to freshwaters can exert detrimental effects on aquatic ecosystems, raising growing concern for both environmental conservation and water security. Current regulation by the EU water framework directive (European Union, 2000/60/EC) relates to organic pollution by monitoring selected micropollutants; however, aquatic ecosystem responses require a comprehensive understanding of dissolved organic matter (DOM) composition. The introduction of high-resolution mass spectrometry (HRMS) is set to greatly increase our understanding of the composition of DOM of both natural and anthropogenic origin derived from diffuse and point sources. METHODS: DOM was extracted from riverine and treated sewage effluent using solid-phase extraction (SPE) and analysed using dissolved organic carbon analysis, direct-infusion high-resolution mass spectrometry (DI-HRMS) and high-performance liquid chromatography (HPLC)/HRMS. The data obtained were analysed using univariate and multivariate statistics to demonstrate differences in background DOM, anthropogenic inputs and in-river mixing. Compound identifications were achieved based on MS2 spectra searched against on-line databases. RESULTS: DI-HRMS spectra showed the highly complex nature of all DOM SPE extracts. Classification and visualisation of extracts containing many thousands of individual compounds were achieved using principal component analysis (PCA) and hierarchical cluster analysis. Kruskal-Wallis analyses highlighted significant discriminating ions originating from the sewage treatment works for more in-depth investigation by HPLC/HRMS. The generation of MS2 spectra in HPLC/HRMS provided the basis for identification of anthropogenic compounds including; pharmaceuticals, illicit drugs, metabolites and oligomers, although many thousands of compounds remain unidentified. CONCLUSIONS: This new approach enables comprehensive analysis of DOM in extracts without any preconceived ideas of the compounds which may be present. This approach has the potential to be used as a high throughput, qualitative, screening method to determine if the composition of point sources differs from that of the receiving water bodies, providing a new approach to the identification of hitherto unrecognised organic contribution to water bodies.

Care bundles in the management of a COPD exacerbation.

Chronic obstructive pulmonary disease (COPD), the umbrella term used to describe chronic lung diseases that cause limitations in lung airflow, is predicted to be the third leading cause of death by 2030. COPD is said to affect 3 million people in the UK, resulting in approximately 30 000 deaths each year. Related healthcare costs continue to escalate, not least because of increasing readmission rates associated with COPD emergencies. The use of care bundles to streamline care is becoming more popular in an attempt to tackle this issue. An integrative literature review was carried out to examine the effectiveness of the use of care bundles. The findings highlighted inconsistencies in the components of bundles, leading to inherent difficulties in assessing which specific component of the bundles led to positive outcomes. The results of this attempt to establish the effectiveness of care bundles in reducing readmission rates and quality of care were inconclusive. The authors recommend further research to investigate the individual components in the bundles and to introduce internationally agreed care bundles for the management of COPD.

LDPE and biodegradable PLA-PBAT plastics differentially affect plant-soil nitrogen partitioning and dynamics in a Hordeum vulgare mesocosm.

Micro and macroplastics are emerging contaminants in agricultural settings, yet their impact on nitrogen (N) cycling and partitioning in plant-soil-microbial systems is poorly understood. In this mesocosm-scale study, spring barley (Hordeum vulgare L.) was exposed to macro or microplastic produced from low density polyethylene (LDPE) or biodegradable plastic at concentrations equivalent to 1, 10 and 20 years of plastic mulch film use. Partitioning of 15N-labelled fertiliser into plant biomass, soil and leachate yielded a partial mass balance. Soil N partitioning was probed via compound-specific 15N-stable isotope analyses of soil microbial protein. Concentration-dependent decreases in plant 15N uptake occurred with increased leached nitrogen for LDPE microplastic. Assimilation into soil microbial protein was higher for biodegradable plastics, which we associate with early-stage biodegradable plastic degradation. Partitioning of 15N into inorganic soil N pools was affected by LDPE size, with lower assimilation into the microbial protein pool. While microplastics and macroplastics altered soil N cycling, the limited impacts on plant health indicated the threshold for negative effects was not reached at agriculturally relevant concentrations. This study highlights the difference between conventional and biodegradable plastics, and emphasises that the interplay of micro and macroplastics on soil N cycling must be considered in future studies.

Increasing concentration of pure micro- and macro-LDPE and PP plastic negatively affect crop biomass, nutrient cycling, and microbial biomass.

Over the last 50 years, the intense use of agricultural plastic in the form of mulch films has led to an accumulation of plastic in soil, creating a legacy of plastic in agricultural fields. Plastic often contains additives, however it is still largely unknown how these compounds affect soil properties, potentially influencing or masking effects of the plastic itself. Therefore, the aim of this study was to investigate the effects of pure plastics of varying sizes and concentrations, to improve our understanding of plastic-only interactions within soil-plant mesocosms. Maize (Zea mays L.) was grown over eight weeks following the addition of micro and macro low-density polyethylene and polypropylene at increasing concentrations (equivalent to 1, 10, 25, and 50 years mulch film use) and the effects of plastic on key soil and plant properties were measured. We found the effect of both macro and microplastic on soil and plant health is negligible in the short-term (1 to <10 years). However, ≥ 10 years of plastic application for both plastic types and sizes resulted in a clear negative effect on plant growth and microbial biomass. This study provides vital insight into the effect of both macro and microplastics on soil and plant properties.

What do macroinvertebrate indices measure? Stressor-specific stream macroinvertebrate indices can be confounded by other stressors.

Monitoring programmes worldwide use biota to assess the "health" of water bodies. Indices based on biota are used to describe the change in status of sites over time, to identify progress against management targets and to diagnose the causes of biological degradation. A variety of numerical stressor-specific biotic indices have been developed based on the response of biota to differences in stressors among sites. Yet, it is not clear how variation in pressures within sites, over what time period, and in what combination has the greatest impact on different biotic groups. An understanding of how temporal variation in pressures influences biological assessment indices would assist in setting achievable targets and help focus catchment-scale mitigation strategies to ensure that they deliver the desired improvements in biological condition.Hydrochemical data provided by a network of high-frequency (15 or 30 min) automated monitoring stations over 3 years were matched to replicated biological data to understand the influence of spatio-temporal variation in pollution pressures on biological indices. Hydrochemical data were summarised in various ways to reflect central tendency, peaks, troughs and variation over 1-90 days before the collection of each biological sample. An objective model selection procedure was used to determine which hydrochemical determinand, and over what time period, best explained variation in the biological indices.Stressor-specific indices derived from macroinvertebrates which purportedly assess stress from low flows, excess fine sediment, nutrient enrichment, pesticides and organic pollution were significantly inter-correlated and reflected periods of low oxygen concentration, even though only one index (ASPTWHPT, average score per taxon) was designed for this purpose. Changes in community composition resulting from one stressor frequently lead to confounding effects on stressor-specific indices.Variation in ASPTWHPT was best described by dissolved oxygen calculated as Q5 over 10 days, suggesting that low oxygen events had most influence over this period. Longer-term effects were apparent, but were masked by recovery. Macroinvertebrate abundance was best described by Q95 of stream velocity over 60 days, suggesting a slower recovery in numbers than in the community trait reflected by ASPTWHPT.Although use of ASPTWHPT was supported, we recommend that additional independent evidence should be used to corroborate any conclusions regarding the causes of degradation drawn from the other stressor-specific indices. The use of such stressor-specific indices alone risks the mistargeting of management strategies if the putative stressor-index approach is taken to be more reliable than the results herein suggest.

Chronic atmospheric reactive N deposition has breached the N sink capacity of a northern ombrotrophic peatbog increasing the gaseous and fluvial N losses.

Peatlands play an important role in modulating the climate, mainly through sequestration of carbon dioxide into peat carbon, which depends on the availability of reactive nitrogen (Nr) to mosses. Atmospheric Nr deposition in the UK has been above the critical load for functional and structural changes to peatland mosses, thus threatening to accelerate their succession by vascular plants and increasing the possibility of Nr export to downstream ecosystems. The N balance of peatlands has received comparatively little attention, mainly due to the difficulty in measuring gaseous N losses as well as the Nr inputs due to biological nitrogen fixation (BNF). In this study we have estimated the mean annual N balance of an ombrotrophic bog (Migneint, North Wales) by measuring in situ N2 + N2O gaseous fluxes and also BNF in peat and mosses. Fluvial N export was monitored through a continuous record of DON flux, while atmospheric N deposition was modelled on a 5 × 5 km grid. The mean annual N mass balance was slightly positive (0.7 ± 4.1 kg N ha-1 y-1) and varied interannually indicating the fragile status of this bog ecosystem that has reached N saturation and is prone to becoming a net N source. Gaseous N losses were a major N output term accounting for 70% of the N inputs, mainly in the form of the inert N2 gas, thus providing partial mitigation to the adverse effects of chronic Nr enrichment. BNF was suppressed by 69%, compared to rates in pristine bogs, but was still active, contributing ~2% of the N inputs. The long-term peat N storage rate (8.4 ± 0.8 kg N ha-1 y-1) cannot be met by the measured N mass balance, showing that the bog catchment is losing more N than it can store due its saturated status.

Identification and quantification of myo-inositol hexakisphosphate in complex environmental matrices using ion chromatography and high-resolution mass spectrometry in comparison to 31P NMR spectroscopy.

Myo-inositol hexakisphosphate, or phytic acid, (myo-IP6) is a key organic phosphorus (P) compound in soils and manures. Determinations of myo-IP6 in soils and manure extracts are frequently performed by 31P NMR spectroscopy. This approach is time-consuming in terms of both sample preparation and instrument time, with uncertainties existing in relation to accuracy of identification and quantification due to potentially interfering resonances from co-extracted P species. In contrast, ion chromatography (IC) in combination with high-resolution mass spectrometry (HRMS) negative ion, electrospray ionisation (ESI) has been shown to enable highly specific identifications of myo-IP6 isolated from complex mixtures. In this paper, IC and ESI-HRMS were applied to the identification and the quantification of myo-IP6 isolated from soils and manures using NaOH-EDTA extraction, and quantifications based on IC. ESI-HRMS analysis of eluate trapped from IC unequivocally confirmed identification of myo-IP6 from a soil extract. The ion suppression cell of the IC instrument provides isolates of the analyte free of ionic components that would interfere with ESI. The myo-IP6 was identified in the NMR by comparing spectra of extracts of soils with and without authentic myo-IP6 "spiked" prior to extraction. Comparison of quantification via standard addition in IC and NMR analysis gave good correlation (r = 0.955). IC with ESI-HRMS was found to be more sensitive, rapid and reliable for the identification and quantification of myo-IP6 with a limit of detection (LOD) of 0.7 mg kg-1 and limit of quantification (LOQ) of 2.1 mg kg-1 using IC versus > 10 mg kg-1 LOD using 31P NMR.

Real-time monitoring of nutrients and dissolved organic matter in rivers: Capturing event dynamics, technological opportunities and future directions.

Excessive riverine nutrient concentrations threaten aquatic ecosystem structure and functioning and can pose substantial risks to human health. Robust monitoring strategies are therefore required to generate reliable estimates of river nutrient loads and to improve understanding of the catchment processes that drive nutrient fluxes. Furthermore, these data are vital for prediction of future trends under changing environmental conditions and thus the development of appropriate mitigation measures. In recent years, technological developments have led to an increase in the use of in-situ nutrient analysers, which enable measurements at far higher temporal resolutions than can be achieved with discrete sampling and subsequent laboratory analysis. In this paper, we review the principles underlying the key techniques used for in-situ nutrient monitoring and highlight both the advantages, opportunities and challenges associated with high-resolution sampling programs. We then suggest how adaptive monitoring strategies, comprising several different temporal sample frequencies, controlled by one or more 'trigger variables' (e.g. river stage, turbidity, or nutrient concentration), can advance our understanding of catchment nutrient dynamics while simultaneously overcoming many of the practical and economic challenges encountered in typical in-situ river nutrient monitoring applications. We present examples of short-term variability in river nutrient dynamics, driven by complex catchment behaviour, which support our case for the development of monitoring systems that can adapt in real-time to rapid changes in environmental conditions. Finally, we suggest future research directions based on emerging technologies in this field.