ERAMMP Report-77: An Air Quality Target for Welsh Ecosystems

Air pollution has impoverished ecosystems in Wales and caused widespread losses of biodiversity. The Welsh Government is assessing the need for a new air quality target (or targets) in relation to ecosystems and biodiversity. A specific target for air quality that can readily be related to effects on ecosystems and biodiversity would help to raise awareness of air pollution impacts. This report briefly reviews air pollution effects on ecosystems and biodiversity, and presents the recommendations of a subgroup of the Clean Air Advisory Panel (CAAP) that was convened in 2022-23 to discuss the issue. The subgroup recommended that a target be set on the basis of a specific single metric, with clearly defined baseline and achievement dates. Air pollutants damage ecosystems through direct toxic effects, and by causing eutrophication (over-fertilisation) and acidification. Ammonia is a particularly damaging air pollutant, with severe effects on many mosses and lichens, and forms a large part of the total nitrogen load that falls on Welsh ecosystems. Other atmospheric pollutants such as ozone or heavy metals may harm ecosystems and biodiversity, but evidence of damage from these is less strong than is evidence for damage from ammonia. Ammonia also contributes to the formation of particulate pollution, which is damaging to wildlife as well as to human health. Ammonia pollution is influenced strongly by emissions from within Wales. The subgroup further recommended that the target be based on: a. Ammonia concentration in air. b. Exceedance of the 1 μg NH3 m-3 annual mean critical level, which is currently exceeded over around 50% of Wales. This level is set to protect sensitive mosses and lichens, which are a valuable component of biodiversity, and contribute to water regulation, peat formation and other ecosystem functions. c. The whole extent of Wales, not only on protected sites or mapped habitat areas. Progress towards the target would need to be assessed primarily using modelled data, which can be provided for the whole area of Wales, and are less influenced by year-to-year variation in meteorology. Calibration of model outputs against ammonia measurements is however important, and the current UK measurement network may not provide sufficient coverage to ensure data accuracy. The specific target metric recommended by the CAAP subgroup is the area of Wales where annual mean concentration of ammonia exceeds the 1 μg m-3 annual mean critical level. A target defined in terms of relative change (for example, a 10% decrease in the area where the critical level is exceeded) would be more robust against changes in the measurement and/or modelling methods than an absolute-change target (for example, 40% of Wales below the critical level). The target value would need to be set after scenario modelling has been carried out to assess what is realistically achievable

Improving sheep feedlot management

This paper summarise six studies undertaken by the Sheep CRC to elucidate certain aspects of confinement feeding of sheep. A review of confinement feeding highlighted the variability of growth rate and feed conversion of sheep and revealed that little is known about the use of sorghum for feeding sheep. The review indicated that the main factors responsible for variation of growth rate and feed conversion were adaptation to grain and feeding system, including the preparation and presentation of feed. The importance of social and physiological adaptation to grain feeding was confirmed. Factors identified as responsible for safe induction and uniform growth rates included prior exposure to grain as lambs, gradual introduction of grain and, when concentrate was provided ad libitum from the first day, the use of either virginiamycin, a pelleted feed, a total mixed ration or a step-wise increase of high-starch grain components. Separate feeding of hay and grain resulted in performance comparable with that of a pelleted diet and that of a total mixed ration. Sorghum-based concentrate diets resulted in growth rates and carcase weights similar to that for winter cereal grains or pellets. Steam flaking or expanding of sorghum had no significant effect on growth rates or carcase weights. These results can be used to determine the profitability of various feedlotting options

Improving sheep feedlot management

This paper summarise six studies undertaken by the Sheep CRC to elucidate certain aspects of confinement feeding of sheep. A review of confinement feeding highlighted the variability of growth rate and feed conversion of sheep and revealed that little is known about the use of sorghum for feeding sheep. The review indicated that the main factors responsible for variation of growth rate and feed conversion were adaptation to grain and feeding system, including the preparation and presentation of feed. The importance of social and physiological adaptation to grain feeding was confirmed. Factors identified as responsible for safe induction and uniform growth rates included prior exposure to grain as lambs, gradual introduction of grain and, when concentrate was provided ad libitum from the first day, the use of either virginiamycin, a pelleted feed, a total mixed ration or a step-wise increase of high-starch grain components. Separate feeding of hay and grain resulted in performance comparable with that of a pelleted diet and that of a total mixed ration. Sorghum-based concentrate diets resulted in growth rates and carcase weights similar to that for winter cereal grains or pellets. Steam flaking or expanding of sorghum had no significant effect on growth rates or carcase weights. These results can be used to determine the profitability of various feedlotting options

Puf3p induces translational repression of genes linked to oxidative stress

In response to stress, the translation of many mRNAs in yeast can change in a fashion discordant with the general repression of translation. Here, we use machine learning to mine the properties of these mRNAs to determine specific translation control signals. We find a strong association between transcripts acutely translationally repressed under oxidative stress and those associated with the RNA-binding protein Puf3p, a known regulator of cellular mRNAs encoding proteins targeted to mitochondria. Under oxidative stress, a PUF3 deleted strain exhibits more robust growth than wild-type cells and the shift in translation from polysomes to monosomes is attenuated, suggesting puf3Δ cells perceive less stress. In agreement, the ratio of reduced:oxidized glutathione, a major antioxidant and indicator of cellular redox state, is increased in unstressed puf3Δ cells but remains lower under stress. In untreated conditions, Puf3p migrates with polysomes rather than ribosome-free fractions, but this is lost under stress. Finally, reverse transcriptase-polymerase chain reaction (RT-PCR) of Puf3p targets following affinity purification shows Puf3p-mRNA associations are maintained or increased under oxidative stress. Collectively, these results point to Puf3p acting as a translational repressor in a manner exceeding the global translational response, possibly by temporarily limiting synthesis of new mitochondrial proteins as cells adapt to the stress

Bell inequalities and entanglement in solid state devices

Bell-inequality checks constitute a probe of entanglement -- given a source of entangled particles, their violation are a signature of the non-local nature of quantum mechanics. Here, we study a solid state device producing pairs of entangled electrons, a superconductor emitting Cooper pairs properly split into the two arms of a normal-metallic fork with the help of appropriate filters. We formulate Bell-type inequalities in terms of current-current cross-correlators, the natural quantities measured in mesoscopic physics; their violation provides evidence that this device indeed is a source of entangled electrons.Comment: 4 pages, 1 figur

Plasma Aβ42/40 ratio, p‐tau181, GFAP, and NfL across the Alzheimer's disease continuum: A cross‐sectional and longitudinal study in the AIBL cohort

Introduction Plasma amyloid beta (Aβ)1-42/Aβ1-40 ratio, phosphorylated-tau181 (p-tau181), glial fibrillary acidic protein (GFAP), and neurofilament light (NfL) are putative blood biomarkers for Alzheimer's disease (AD). However, head-to-head cross-sectional and longitudinal comparisons of the aforementioned biomarkers across the AD continuum are lacking. Methods Plasma Aβ1-42, Aβ1-40, p-tau181, GFAP, and NfL were measured utilizing the Single Molecule Array (Simoa) platform and compared cross-sectionally across the AD continuum, wherein Aβ-PET (positron emission tomography)–negative cognitively unimpaired (CU Aβ−, n = 81) and mild cognitive impairment (MCI Aβ−, n = 26) participants were compared with Aβ-PET–positive participants across the AD continuum (CU Aβ+, n = 39; MCI Aβ+, n = 33; AD Aβ+, n = 46) from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL) cohort. Longitudinal plasma biomarker changes were also assessed in MCI (n = 27) and AD (n = 29) participants compared with CU (n = 120) participants. In addition, associations between baseline plasma biomarker levels and prospective cognitive decline and Aβ-PET load were assessed over a 7 to 10-year duration. Results Lower plasma Aβ1-42/Aβ1-40 ratio and elevated p-tau181 and GFAP were observed in CU Aβ+, MCI Aβ+, and AD Aβ+, whereas elevated plasma NfL was observed in MCI Aβ+ and AD Aβ+, compared with CU Aβ− and MCI Aβ−. Among the aforementioned plasma biomarkers, for models with and without AD risk factors (age, sex, and apolipoprotein E (APOE) ε4 carrier status), p-tau181 performed equivalent to or better than other biomarkers in predicting a brain Aβ−/+ status across the AD continuum. However, for models with and without the AD risk factors, a biomarker panel of Aβ1-42/Aβ1-40, p-tau181, and GFAP performed equivalent to or better than any of the biomarkers alone in predicting brain Aβ−/+ status across the AD continuum. Longitudinally, plasma Aβ1-42/Aβ1-40, p-tau181, and GFAP were altered in MCI compared with CU, and plasma GFAP and NfL were altered in AD compared with CU. In addition, lower plasma Aβ1-42/Aβ1-40 and higher p-tau181, GFAP, and NfL were associated with prospective cognitive decline and lower plasma Aβ1-42/Aβ1-40, and higher p-tau181 and GFAP were associated with increased Aβ-PET load prospectively. Discussion These findings suggest that plasma biomarkers are altered cross-sectionally and longitudinally, along the AD continuum, and are prospectively associated with cognitive decline and brain Aβ-PET load. In addition, although p-tau181 performed equivalent to or better than other biomarkers in predicting an Aβ−/+ status across the AD continuum, a panel of biomarkers may have superior Aβ−/+ status predictive capability across the AD continuum

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions

The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: ‘archetypal’ transcriptional blocks that are regulated in a concerted fashion in response to external stimuli

The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation

Translation initiation factor eIF4E mediates mRNA selection for protein synthesis via the mRNA 5’cap. A family of binding proteins, termed the 4E-BPs, interact with eIF4E to hinder ribosome recruitment. Mechanisms underlying mRNA specificity for 4E-BP control remain poorly understood. Saccharomyces cerevisiae 4E-BPs, Caf20p and Eap1p, each regulate an overlapping set of mRNAs. We undertook global approaches to identify protein and RNA partners of both 4E-BPs by immunoprecipitation of tagged proteins combined with mass spectrometry or next-generation sequencing. Unexpectedly, mass spectrometry indicated that the 4E-BPs associate with many ribosomal proteins. 80S ribosome and polysome association was independently confirmed and was not dependent upon interaction with eIF4E, as mutated forms of both Caf20p and Eap1p with disrupted eIF4E-binding motifs retain ribosome interaction. Whole-cell proteomics revealed Caf20p mutations cause both up and down-regulation of proteins and that many changes were independent of the 4E-binding motif. Investigations into Caf20p mRNA targets by immunoprecipitation followed by RNA sequencing revealed a strong association between Caf20p and mRNAs involved in transcription and cell cycle processes, consistent with observed cell cycle phenotypes of mutant strains. A core set of over 500 Caf20p-interacting mRNAs comprised of both eIF4E-dependent (75%) and eIF4E-independent targets (25%), which differ in sequence attributes. eIF4E-independent mRNAs share a 3’ UTR motif. Caf20p binds all tested motif-containing 3’ UTRs. Caf20p and the 3’UTR combine to influence ERS1 mRNA polysome association consistent with Caf20p contributing to translational control. Finally ERS1 3’UTR confers Caf20-dependent repression of expression to a heterologous reporter gene. Taken together, these data reveal conserved features of eIF4E-dependent Caf20p mRNA targets and uncover a novel eIF4E-independent mode of Caf20p binding to mRNAs that extends the regulatory role of Caf20p in the mRNA-specific repression of protein synthesis beyond its interaction with eIF4E

Scoping future research for air pollution recovery indicators (APRI). (Workshop report)

Atmospheric nitrogen (N) pollution is a major and ongoing cause of biodiversity loss across the UK, but in some locations N pollution pressures have been declining. In response to these dynamics, JNCC requested a workshop to help to scope Phase 2 of the Air Pollution Recovery Indicators (APRI) project. The damaging effects of excess N load and of gaseous ammonia on many ecosystems are clear. However, the processes and timescales of ecosystem recovery following a decrease in pollution pressure are less well understood. The APRI project aims to take practical steps to fill this knowledge gap by delivering new scientific research focused on indicators of ecosystem and species recovery from N pollution. In Phase 1, predominantly below-ground responses are being studied at a dry heathland site where experimental additions of N were made between 1998 and 2011, revealing lingering effects on soil chemistry, the soil fungi community and vegetation structure (Kowal et al. 2024). The effect on mycorrhizal fungi, and using these fungi as recovery indicators, is being examined in more detail with recently established assessment methods (Arrigoni et al. 2023). Phase 2 of APRI will consider recovery from N impacts more broadly, e.g. by studying other habitats or species. Further empirical research may be commissioned to better understand recovery pathways from air pollution. A workshop was held on 7–8 November 2023 to help develop an action plan for the remainder of the APRI project. This report summarises the workshop discussion and ensuing work. We note that the focus of the APRI project is on assessing recovery. It is therefore essential to contrast responses of ecosystems subject to decreased pollution pressure with indicators from ecosystems experiencing ongoing pollution. Properties that have been used previously to assess impacts can be used to understand recovery, and novel indicators of ecosystem change are also likely to be useful for assessing recovery. Whatever indicators are chosen to assess change, benchmarking data will be needed to assess the range of potential values and relationships with N deposition. Results from the workshop and subsequent discussions include: • Eleven criteria to help choose appropriate indicators in relation to declining N deposition: Speed of response, Sensitivity of response, Specificity of response, Generality to multiple habitats, Relatedness to recovery endpoints, Previous use, Breadth of pollution gradient, Added value to other policy areas, Resilience in face of anticipated change, Feasibility of collection, Measurement uncertainty. • The need to consider a basket of indicators to indicate recovery from N pollution. Such a basket could include examples from different categories e.g. indicators of pressure, biogeochemical response indicators, and biotic response indicators, with individual indicators likely responding over different timescales. The exact choice may depend on the habitat concerned and the availability of prior data, as well as the question being posed and/or policy goal. • Explicit recommendations on sites to target in APRI Phase 2 to gain information on recovery indicator trajectories, namely (i) well-designed field experiments where N addition has ceased, and (ii) point sources of emissions that have ceased to operate, preferably with a super-imposition of an experimental treatment or treatments. Given uncertainties associated with modelled historical, contemporary, and future N deposition and the potential for confounding variables, analysing survey data from across the UK will be unlikely to provide robust information within the timeframes of the APRI Phase 2. We recommend further assessments may help develop detailed plans for empirical work in Phase 2 of APRI. Potential next steps are to: • Finalise a list of potential and priority indicators of recovery from air pollution (which may differ by habitat type), specifically from high levels of N deposition and/or high atmospheric reactive N concentrations. This finalisation could be done through active participation of the air pollution community and the completion of ‘live’ spreadsheets that address potential indicator criteria. • Summarise relevant data on recovery indicators, across key semi-natural habitats. This summary should include data available from other countries with similar environmental contexts, to help disentangle drivers of change in the UK context. This evidence will help understand recovery pathways from air pollution. As above, this could be done through the active participation of the air pollution community and the completion of ‘live’ spreadsheets. Such an approach could also enable gap analyses, for example identifying where we are missing information by habitat and/or environmental conditions. • Identify areas where co-located monitoring of N with existing habitat/species monitoring could enhance the likelihood for establishing recovery indicators. This should enhance other similar activity such as through the Natural Capital and Ecosystem Assessment programme and the UK Air Pollution Impacts on Ecosystems Networks (APIENs). • Develop a list of priority habitats and sites where empirical research is needed to better understand recovery pathways, including a gap analysis of habitats, methods and/or indicators. • Encourage activities that enhance understanding of ammonia emission sources at local scale (e.g. 1 km or less), to help better identify areas where N pollution has decreased, and recovery might be detected. This could include intensive monitoring or collating and sharing information about permitted N sources. • Develop case studies, including potentially from APRI Phase 1, to demonstrate how existing evidence on localised recovery in semi-natural habitats of conservation importance can be used by policy- and decision-makers to help drive policy toward continued reductions in emissions of reactive N