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Forests under elevated atmospheric CO2 concentration as a result of climate change are expected to require more available nitrogen (N) to sustain the enhanced CO2 uptake for photosynthesis and C storage. Therefore, it is essential to evaluate how CO2 fumigation of forests will affect availability of N to trees. Main pathways to sustain the high N demand are increasing biological N fixation (BNF), increasing N turn-over and reducing N losses. The purpose of this research is to explore the effects of elevated CO2 on soil N cycling in a temperate forest under the Birmingham Institute of Forest Research (BIFoR) Free Air Carbon Dioxide Enrichment (FACE) facility. We hypothesize that under CO2 fertilization, trees will allocate more carbon belowground to enhance microbial activity resulting in an increase of all nitrogen fluxes (i.e. N mineralisation, N fixation and N gas emissions). Net mineralisation rates were measured in-situ every month over 10 months and gross mineralisation rates were measured in-situ in spring, summer and autumn using the 15N pool dilution method. BNF by free-living organisms was investigated using the 15N assimilation method and N2O production rates were measured using the 15N-Gas flux method. Net mineralisation was increased on average by 30% under elevated CO2, delivering an extra 24 kgN.ha-1.y-1, and by 80% during the budburst period (April). Gross ammonification and NH4+ immobilisation rates were also slightly higher under elevated CO2 by respectively 33% and 19%. Yet, nitrification, NO3 immobilisation and N2O emission rates were not affected, demonstrating that, ammonium and nitrate cycling responded differently to elevated CO2. In addition, under elevated CO2, soils were more concentrated in DOC, DON and ammonium (p

Leaf-level transpiration is an indicator of tree species’ response to soil water status and atmospheric conditions and is known to vary in response to photosynthetic radiation at a sub minute timescale. Here we report results from replicate measurement of stomatal conductance to water over 30 second intervals using a porometer, and leaf vapour pressure deficit (VPDleaf), requiring measurement of abaxial leaf temperature. At Birmingham Institute of Forest Research (BIFoR) Free-Air CO2 Enrichment (FACE) forest in Staffordshire UK, we use leaf-level transpiration data during leaf-on season (May to October) to explore diurnal tree water usage results from 18 mature oaks (Quercus robur L.) under elevated CO2 conditions. In six of our nine experimental arrays (3 patches with elevated CO2 infrastructure (eCO2); 3 with infrastructure but ambient CO2 (aCO2)) we accessed the top tree canopy of one tree per array during full leaf-on months over three years from 2019-2021 to measure stomatal conductance using a porometer and pre-measurement of abaxial leaf temperature. We compare the results between treatments to determine the effects of elevated CO2 on stomatal regulation, to predict the dynamics of leaf level transpiration and the relationship to whole tree water usage determined from sap flux measurements, underpinning previously reported results of both water usage, and of carbon assimilation measured at leaf level using a Licor chamber method. An alternative porometric transpiration measurement method, using cut twig samples, was adopted for three trees in the final three control arrays (3 ‘ghosts’ (no treatment, no infrastructure)) during 2018-2021 as limited in-situ access to top canopy was available via arborists. Cut twig samples from infrastructure arrays were also measured during 2019-2021. We compare leaf-level stomatal conductance results sub-diurnally to our previously reported stem sap flux and water usage responses from stem sap transducers (whole canopy) measures in the same trees. Maximum sap flux rates (ca. 0.04 litres s-1) occur around midday (UTC) and predict that tree radius and canopy area determine variability of total water usage per tree per day across this tree radius range (ca. 2.4 litres per millimetre radius, range; 274mm £ radius £ 465 mm). We report a delayed response in the water flows in the stem relative to the leaf (from the in-situ measurements), implying a buffering factor relating to the height and age of the trees studied and use of stored water at branch level. We note the differences and limitations of measuring transpiration by porometry from cut twigs. Interpretation of these results, from our tree-centred forest view, provide further understanding of future-forest tree-based water usage which can be expanded to predict responses at ecosystem levels, contribute to development of more realistic vegetation models and identify optimum methods for canopy leaf transpiration measurement in forest wide experiments.

Anthropogenic CO2 emissions have resulted in elevated CO2 (eCO2) in the atmosphere, and this rise is predicted to continue1. Increases in CO2 have fertilised forest ecosystems and led to an uptake of CO2 into plant and soil biomass. Early findings at BIFoR FACE (Free-Air Carbon Dioxide Enrichment) showed increased photosynthetic uptake2, fine root net primary productivity3 and soil respiration4, indicating increased carbon (C) allocation belowground and mirroring previous forest FACE experiments. Roots play a key role in whole-plant functions, biogeochemical cycling and interactions with biotic factors, thus based on the early findings we expect that the increased C allocation belowground will have an impact on root biomass and architecture. Root biomass combined with root architecture (such as root diameter and length) are of high importance to elucidate the impacts of eCO2 on primary productivity, interactions in the rhizosphere, carbon sequestration and nutrient cycling5,6. This study assesses the impact of elevated CO2 on root biomass and architecture at the BIFoR FACE the first 5 years of operation (2017-2022). Changes in root biomass and architecture were monitored via soil coring three times a year (spring, summer and autumn) to 30 cm (per horizon). The root biomass in assessed as per dry weight in four different root diameter classes (5 mm) and the root architecture was assessed via fresh root scanning. Root biomass exhibited a prompt and sustained increase under eCO2 during the first 5 years of CO2 fumigation, with the increase being more pronounced for the three smaller diameter classes (5 mm). Increases in root biomass could suggest increases in total root length, root diameter and tissue density, enhancing trees’ capacity to acquire more soil resources such as water and nutrients, or resource storage. References1Intergovernmental Panel on Climate Change; Core Writing Team; Pachauri, R.K.; Meyer, L.A. (Eds.) Climate Change 2014: Synthesis Report, Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change; Intergovernmental Panel on Climate Change: Geneva, Switzerland, 2014; 151p.2Gardner, A., Ellsworth, D., Crous, K., Pritchard, J., Mackenzie, A.R. (2021). Is photosynthetic enhancement sustained through three years of elevated CO2 exposure in 175-year-old Quercus robur? Tree Physiology, 42 (1), 130-1443Ziegler, C., Kulawska, A., Kourmouli, A., Hamilton, L., Shi, Z., MacKenzie, A.R., Dyson, R.J., Johnston, I.G. (2022). Quantification and uncertainty of root growth stimulation by elevated CO2 in mature temperate deciduous forest. Science of the Total Environment, 854,4Kourmouli, A., Hamilton, L., Pihlblad, J., Barba, J., Bartlett, R., MacKenzie, AR., Hartley, I., Shi, Z. (2023). Initial carbon and nutrient responses to free air CO2 enrichment in a mature deciduous woodland. (submitted) 5Norby, R. J., & Jackson, R. B. (2000). Root dynamics and global change: Seeking an ecosystem perspective. New Phytologist, 147, 3–12.6Wilson, S. D. (2014). Below-ground opportunities in vegetation science. Journal of Vegetation Science, 25, 1117–1125.

Pollen allergies affect a significant proportion of the global population, and this is expected to worsen in years to come. There is demand for the development of automated pollen monitoring systems to progress from conventional manual sampling techniques. Low-cost Optical Particle Counters (OPCs) are conventionally used for measuring particulate matter and have attractive advantages of real-time high time resolution data and affordable costs. Our study asks whether low-cost OPC sensors be used for meaningful monitoring airborne pollen and utilises data from the EUMETNET Autopollen ADOPT – COST Action Intercomparison Campaign (2021) in Munich, Germany.We employ a variety of methods, including supervised machine learning techniques, to construct pollen proxies from hourly-average OPC data and evaluate their performance. The most successful methods are supervised machine learning Neural Network (NN) and Random Forest (RF) methods, trained from pollen concentrations collected from a Hirst-type sampler. These perform significantly better than using a simple particle size-filtered proxy or a Positive Matrix Factorisation (PMF) source apportionment pollen proxy. We developed a collection of models - varying by model type, input features (including particle size and meteorological data) and target variable (i.e. total pollen vs selected pollen taxa) - and evaluated their suitability for constructing a pollen proxy. The results show that such models can construct useful information on pollen from OPC particle size data with Spearman correlation coefficients up to 0.85 and coefficients of determination up to 0.67. Model-constructed proxies demonstrated an ability to distinguish high pollen events with promising results (F1 Scores up to 0.83) and to follow monthly and diurnal trends in pollen. We discuss the suitability of OPCs for monitoring pollen and offer advice for future progress. We demonstrate an attractive alternative for automated pollen monitoring that could provide valuable and timely information to the benefit of pollen allergy sufferers.

Pollen are hygroscopic and so have the potential to act as cloud condensation nuclei (CCN) in the atmosphere. This could have yet uncertain implications for cloud processes and climate. Previous studies have investigated the hygroscopic swelling of pollen, linked to CCN activity by the κ-Köhler theory, using methods that follow observed mass increase by electrodynamic balance (EDB) or vapour sorption analyser. This study uses an acoustic levitator to levitate pollen grains in the true aerosol phase and uses a macroscope to image the pollen to investigate hygroscopic behaviour when relative humidity (RH) is changed. Two pollen species were studied in this work: Lilium orientalis (oriental lily) and Populus deltoides (eastern cottonwood). Both species were successfully levitated, however, the smaller Populus deltoides showed greater instability throughout experiments. The quality of images taken by the macroscope, and thus calculations of pollen area and diameter ratio, varied significantly and were sensitive to lighting conditions, as well as levitated pollen grain movement and orientation. Experiments with surface-fixed pollen grains were also conducted. They showed evidence that pollen hygroscopic swelling could be observed by the macroscope. The produced results were comparable with previously reported mass increase values. Although less accurate than methods that measure mass changes, the acoustic levitator and macroscope setup offer an attractive alternative by virtue of being commercial-off-the-shelf, low-cost, and versatile. A key advantage of this method is that it is possible to visually observe particle shape dynamics under varying environmental conditions.

Increasing CO2 levels are a major global challenge, and the potential mitigation of anthropogenic CO2 emissions by natural carbon sinks remains poorly understood. The uptake of elevated CO2 (eCO2) by the terrestrial biosphere, and subsequent sequestration as biomass in ecosystems, remain hard to quantify in natural ecosystems. Here, we combine field observations of fine root stocks and flows, derived from belowground imaging and soil cores, with image analysis, stochastic modelling, and statistical inference, to elucidate belowground root dynamics in a mature temperate deciduous forest under free-air eCO2 to 150 ppm above ambient levels. eCO2 led to relatively faster root production (a peak volume fold change of 4.52 ± 0.44 eCO2 versus 2.58 ± 0.21 control), with increased root elongation relative to decay the likely causal mechanism for this acceleration. Physical analysis of 552 root systems from soil cores support this picture, with lengths and widths of fine roots significantly increasing under eCO2. Estimated fine root contributions to belowground net primary productivity increase under eCO2 (mean annual 204 ± 93 g dw m−2 yr−1 eCO2 versus 140 ± 60 g dw m−2 yr−1 control). This multi-faceted approach thus sheds quantitative light on the challenging characterisation of the eCO2 response of root biomass in mature temperate forests. publishedVersion

This study was funded by an investigator-initiated research grant from Insmed (Bridgewater, NJ, USA). The authors acknowledge the funding and logistical support from the UK National Institute for Health and Care Research. Background: Neutrophil serine proteases are involved in the pathogenesis of COVID-19 and increased serine protease activity has been reported in severe and fatal infection. We investigated whether brensocatib, an inhibitor of dipeptidyl peptidase-1 (DPP-1; an enzyme responsible for the activation of neutrophil serine proteases), would improve outcomes in patients hospitalised with COVID-19. Methods: In a multicentre, double-blind, randomised, parallel-group, placebo-controlled trial, across 14 hospitals in the UK, patients aged 16 years and older who were hospitalised with COVID-19 and had at least one risk factor for severe disease were randomly assigned 1:1, within 96 h of hospital admission, to once-daily brensocatib 25 mg or placebo orally for 28 days. Patients were randomly assigned via a central web-based randomisation system (TruST). Randomisation was stratified by site and age (65 years or ≥65 years), and within each stratum, blocks were of random sizes of two, four, or six patients. Participants in both groups continued to receive other therapies required to manage their condition. Participants, study staff, and investigators were masked to the study assignment. The primary outcome was the 7-point WHO ordinal scale for clinical status at day 29 after random assignment. The intention-to-treat population included all patients who were randomly assigned and met the enrolment criteria. The safety population included all participants who received at least one dose of study medication. This study was registered with the ISRCTN registry, ISRCTN30564012. Findings: Between June 5, 2020, and Jan 25, 2021, 406 patients were randomly assigned to brensocatib or placebo; 192 (47·3%) to the brensocatib group and 214 (52·7%) to the placebo group. Two participants were excluded after being randomly assigned in the brensocatib group (214 patients included in the placebo group and 190 included in the brensocatib group in the intention-to-treat population). Primary outcome data was unavailable for six patients (three in the brensocatib group and three in the placebo group). Patients in the brensocatib group had worse clinical status at day 29 after being randomly assigned than those in the placebo group (adjusted odds ratio 0·72 [95% CI 0·57-0·92]). Prespecified subgroup analyses of the primary outcome supported the primary results. 185 participants reported at least one adverse event; 99 (46%) in the placebo group and 86 (45%) in the brensocatib group. The most common adverse events were gastrointestinal disorders and infections. One death in the placebo group was judged as possibly related to study drug. Interpretation: Brensocatib treatment did not improve clinical status at day 29 in patients hospitalised with COVID-19. Publisher PDF

Increasing CO

The capacity to predict NO

In forests, air-parcel residence times – the inverse of first-order exchange rates – influence in-canopy chemistry and the exchanges of momentum, energy, and mass with the surrounding atmosphere. Accurate estimates are needed for chemical investigations of reactive trace species, such as volatile organic compounds, some of whose chemical lifetimes are in the order of average residence times. However, very few observational residence-time estimates have been reported. Little is known about even the basic statistics of real-world residence times or how they are influenced by meteorological variables such as turbulence or atmospheric stability. Here, we report opportunistic investigations of air-parcel residence times in a free-air carbon dioxide enrichment (FACE) facility in a mature, broadleaf deciduous forest with canopy height hc ≈ 25 m. Using nearly 50 million FACE observations, we find that median daytime residence times in the tree crowns range from around 70 s when the trees are in leaf to just over 34 s when they are not. Air-parcel residence times increase with increasing atmospheric stability, as does the dispersion around their central value. Residence times scale approximately with the reciprocal of the friction velocity, u*. During some calm evenings in the growing season, we observe distinctly different behaviour: pooled air being sporadically and unpredictably vented – evidenced by sustained increases in CO2 concentration – when intermittent turbulence penetrates the canopy. In these conditions, the concept of a residence time is less clearly defined. Parameterisations available in the literature underestimate turbulent exchange in the upper half of forest crowns and overestimate the frequency of long residence times. Robust parametrisations of air-parcel residence times (or, equivalently, fractions of emissions escaping the canopy) may be generated from inverse gamma distributions, with the parameters 1.4 ≤ α ≤ 1.8 and β = hc / u* estimated from widely measured flow variables. In this case, the mean value for τ becomes formally defined as 𝜏̅ = β / (α−1). For species released in the canopy during the daytime, chemical transformations are unlikely unless the reaction time scale is in the order of a few minutes or less.

Cities intimately intermingle people and air pollution. However, is very difficult to assess the efficacy of air pollution policy. Permanent in-situ observations are usually too sparsely spaced to monitor transport processes within a city. The post-processing and maintenance costs associated with calibrated low-cost sensors remains too high for them simply to fill the gaps in permanent networks. The behaviour of pollutants around the scale of a neighbourhood (1-2km) remains particularly difficult to interpret and model. This gap in our understanding is unfortunate because neighbourhood-scale processes disperse pollutants from peaks beside busy roads to levels treated as the ‘urban background’, and may link urban pollution models with weather forecasts.Urban areas can be treated as patches of porous media to which the wind adjusts by changing its mean and turbulent components. Most cities around the world are made up of lots of neighbourhoods of differing form, density and land use – e.g. commercial centres interspaced with low-rise residential neighbourhoods. For cities whose urban form varies in this way, we formulated two neighbourhood-scale flow regimes, based on the size and density of the different neighbourhood patches.We used large-eddy simulation to investigate how these two dynamical regimes emerge in patchy neighbourhoods, and their implications for pollution policy and research. We found that these flow regimes distribute pollutants in counter-intuitive ways, such as producing pollution ‘hot spots’ in less dense patches. The flow regimes also provide: (a) a quantitative definition of the ‘urban background’, which can be used for more precisely targeted pollution monitoring; and (b) a conceptual basis for neighbourhood-scale air pollution problems and transport of fluid constituents in other porous media.

Recent research highlights the ability of large trees to maintain transpiration during tree water stress, for example in summer dry periods, by using stored plant water held in the relaxed xylem. Use of soil water at different depths by shallow and deep roots according to soil water content may also vary by species and seasonal climatic conditions to maintain transpiration demands. Here we present daylight tree water usage measurements of mature oaks (Quercus robur L.) under future-forest CO2 conditions, derived from compensation heat pulse (HPC) xylem sap flux transducers deployed at Birmingham Institute of Forest Research (BIFoR) Free-Air CO2 Enrichment (FACE) forest in Staffordshire UK. We experienced longer dry periods in summers 2018 and 2019 and variable annual summer precipitation overall. Xylem sap flux data is collected half-hourly from eighteen oak trees and a smaller number of subdominant trees (Acer pseudoplatanus and Crataegus monogyna) in nine experimental patches: 3 patches with elevated CO2 infrastructure (eCO2); 3 with infrastructure but ambient CO2 (aCO2); and 3 ‘ghosts’ (no treatment, no infrastructure). Each tree has two probesets, E and W facing; long (7 cm 4-sensor) probes in oak and short (4cm 2-sensor) probes, to accommodate the smaller diameter subdominant trees, are deployed. We compare individual tree responses under the three treatments across the leaf-on seasons for early years of the FACE project 2017–2021. Between-individual within-species variability of summertime monthly average of daily daylight water usage in oak is linearly proportional to tree stem radius (ca. 2.9 litres per millimetre radius, range; 274mm ≥ radius ≤ 465 mm) at the point of probeset insertion ca. 1.1–1.3 m above ground level and oak responds sub-daily to solar radiation reduction events during cloud cover. Diurnal stem sap flux responses to canopy photosynthetic demand typically exhibit increased sap flux from dawn to around midday (UTC) and symmetrical decrease to dusk. We describe our continuing investigation of soil-plant-atmosphere flows, monitoring root-xylem-stomatal changes, and discuss how these results, from our tree-centred forest view, provide valuable new perspectives and help to improve our understanding of future-forest-water use at larger scales, contributing to development of more realistic ecohydrological vegetation, soil and landscape models.

Plants communicate information about their status, intra- and inter- plant, and with other ecosystem members, through the release of volatile organic compounds (VOCs). The effects of rising CO2 in conjunction with ozone (O3) on plant VOC emissions is not yet fully understood, but research suggests that some herbivore-induced VOCs are degraded by O3, potentially reducing their signalling function. Furthermore, elevated CO2 has been shown to attenuate induced VOC responses to herbivory in Brassica oleracea. We are using two tri-trophic model systems; black poplar [Populus nigra betulifolia], winter moth [Operophtera brumata] and a tachinid fly parasitoid of winter moth, Cyzenis albicans; and oil seed rape [Brassica napus], diamond back moth [Plutella xylostella] (DBM), and a parasitoid of DBM, braconid wasp, Cotesia plutella. Additionally, we are working within two ground-breaking facilities; the Birmingham Institute of Forest Research (BIFoR)’s free-air carbon enrichment (FACE) experiment, and University of Reading’s free-air diesel and ozone enrichment experiment. We will also collect some data from lab-based experiments.Our project seeks to characterise the volatile organic compound (VOC) profiles emitted for both plants under herbivory, examine how these VOC profiles differ under combined elevated CO2 and O3, and explore whether changes to VOC profiles impact key ecological relationships, e.g, the ability of plants to signal to herbivore enemies.

According to the Forest European Process, the recent Climate Change Conference (COP26), and EU policies, conservation of forest ecosystems is a critical step in mitigating climate change and combating deforestation; accordingly plantation forests will be critical in achieving these goals. While limitations in monoculture plantation are well established in silvicultural practices and documented in research studies, in the face of intensifying climate change and resources scarcity, the need for knowledge on mixed-species plantations has grown. There has been also a recent develop in innovative and sustainable forest management practices, including irrigation and fertilization (fertigation) that aim to improve the productivity of forestry plantations, and therefore their carbon sequestration capacity, as well as the ecosystem services associated with healthy forests. However, the exact effects of fertigation on forests plantation have yet to be established. This study examines the growth patterns, productivity, and carbon storage capacity of four–year-old mixed-species and monoculture plantations in response to an intensive fertigation management. Particularly, our findings highlight differences in tree growth patterns and their performance in paired experimental plots based on different soil types. Such differences are associated varying soil moisture conditions due the interaction of fertigation and the soil water holding capacity. In general, trees growth is higher in sandy soil, due to the positive relation between high soil water diffusivity and fertigation. On the other hand, no such tree growth has been observed in clay soil, most likely due to the high susceptibility to waterlogging, which requires careful fertigation management to avoid limiting conditions for the healthy development of young forest plantation. Our research provides important insights into how young plantation trees respond to different soil moisture conditions, which can aid to in the design and fertigation management of mixed-species plantations resulting in more productive, biodiverse, economically viable, and healthier forests than monocultures.

Forests under elevated atmospheric CO2 concentration as a result of climate change are expected to require more available nitrogen (N) to sustain the enhanced CO2 uptake for photosynthesis and C storage. Therefore, it is essential to evaluate how CO2 fumigation of forests will affect availability of N to trees. Main pathways to sustain the high N demand are increasing biological N fixation (BNF), increasing N turn-over and reducing N losses. The purpose of this research is to explore the effects of elevated CO2 on soil N cycling in a temperate forest under the Birmingham Institute of Forest Research (BIFoR) Free Air Carbon Dioxide Enrichment facility. We hypothesize that under CO2 fertilization, trees will allocate more carbon belowground to enhance microbial activity for increasing N mineralization as well as enhancing BNF to meet N demands. We also hypothesize that the subsequent microbial activity will up-regulate N2O and N2 emissions due to denitrification. BNF by free-living organisms is investigated using the 15N assimilation method. Mineralization and N gas production rates is determined using the 15N pool dilution and 15N-Gas flux method at the same time. Early results are showing trends toward an enhancement of N mineralization and microbial N immobilization rates. However, BNF in the forest floor is hardly detectable more likely because of the high N deposition in the area; therefore, it doesn’t appear to be responsive to CO2 fumigation. This research is expected to help us improve our understanding of the changes and magnitude of nutrient availability and gaseous losses under future climates.

The benefits of ‘green infrastructure’ are multi-faceted and well-documented, but estimating those of individual street-scale planting schemes at planning can be challenging. This is crucial to avoid undervaluing proposed schemes in cost–benefit analyses, and ensure they are resilient to ‘value engineering’ between planning and implementation. Here, we introduce prototype software enabling urban practitioners to estimate the site-specific air quality impacts of roadside vegetation barriers: highly localised changes in pollutant concentrations due to changes in the dispersion of vehicular emissions close to source. We summarise the recent shift in understanding regarding the impacts of vegetation on urban air pollution towards changes in pollutant dispersion (cf. deposition) and describe our prototype software, offering rapid estimates thereof. First tests of the underlying model’s performance are promising, reproducing: annual mean NO2 and PM2.5 concentrations in a street canyon (Marylebone Road, London, UK) to within 10% and 25%, respectively, and changes in pollutant concentrations of the right order of magnitude behind roadside barriers in a wind tunnel simulation of a street canyon and a real open-road environment. However, the model underestimates the benefits of a barrier in a simulated street canyon under perpendicular wind conditions. The prototype software is a first step towards informing practitioners of the site-specific impacts of vegetation barriers, which should always be additional to (i.e., no substitute for) essential emission reductions. The code is open-source to engage further researchers in its continued development.

The timings of phenological events play an important role in determining the annual carbon uptake in key terrestrial carbon sinks, such as mature forests. With increases in atmospheric CO2 expected to change physiological processes in plants, it is becoming increasingly important to monitor the changes in plant traits and subsequent phenological changes that may occur. Changes in photosynthetic pigments, such as chlorophyll, can be used as a proxy for physiological changes in leaves and can therefore be useful to monitor potential phenological change, such as autumnal leaf senescence. Non-destructive techniques allow for measurements of photosynthetic pigments without destructive sampling that would disturb the canopy. These methods are particularly useful in logistically difficult environments, such as high forest, or remote environments where traditional chlorophyll extractions are problematic and serve as ground-truthing for remote sensing of greenness. In the present study, we aimed to assess the effects of elevated CO2 (150 mmol mol-1 above ambient) and canopy position on chlorophyll concentrations of a common canopy-dominant species to identify potential implications on phenology. The study was conducted in a mature temperate forest situated at a Free Air Carbon Enrichment (FACE) experiment in the UK. Over 5,000 in-situ chlorophyll measurements were collected, across the 3rd and 4th season of CO2 fumigation, in the canopy-dominant species Quercus robur (Q. robur). Additionally, 100 leaves were destructively sampled to verify chlorophyll concentrations using traditional chlorophyll extraction techniques. The established relationship between chlorophyll absorptance readings and leaf chlorophyll content allowed robust species-specific calibration equations to be calculated. Consistent with previous work, this study observed significantly higher chlorophyll concentrations at lower positions in the canopy in both sampling years (P < 0.001). Additionally, a reduction in foliar chlorophyll concentrations (-2 to -9%) when exposed to eCO2 in both sampling years was observed, but this was only significant for the upper canopy (-7 to -9%, P < 0.05). This study found a marginally significant effect of CO2 treatment on reducing the effective season length, with larger eCO2-induced reductions in chlorophyll occurred through autumn. Overall, the research highlights a simple non-invasive method for monitoring changes in leaf traits of mature trees under eCO2. The results suggest that leaves may be able to reallocate their resources away from light-harvesting apparatus in response to eCO2, particularly in the upper canopy. Furthermore, the findings suggest direct consequences of rising atmospheric CO2 to potential alterations of phenological events, such as leaf senescence, that may have implications for forest productivity and adaptation in a future high CO2 world. Additionally, the research has shown the need to monitor potential changes in resource allocation to photosynthetic apparatus across the season as atmospheric CO2 continues to rise. The information obtained in this study can be used to increase accuracy in the modelling of climate-carbon scenarios.

Boreal forests are located at latitudes that are predicted to experience some of the greatest warming on the planet. Forests growing on permafrost may be particularly vulnerable, with accelerated soil warming and permafrost degradation linked to changing patterns of tree growth and longevity. Many have speculated that thawing permafrost, through its effects on soil water content and ground stability, will increase forest mortality across the boreal region. However, recent evidence indicates mixed forest responses to permafrost thaw. In some areas, the onset of thaw is followed by increased tree growth and increased forest cover area. In other sites, thaw has been linked to decreased growth and forest cover loss. It is currently poorly understood what determines these contrasting responses, and the roles that different environmental and climatic factors may play. This leads to two major issues: (1) uncertainties in predicting the effects of future permafrost thaw on carbon dynamics in northern ecosystems, and (2) poor understanding of where scientific and conservation efforts should be focused. Here, we present a review of the recent evidence of permafrost thaw effects on boreal forest dynamics and propose an explanation for the differing responses across sites. We argue that the outcome is controlled by a set of factors that influence two major pathways and the interactions between them: (1) permafrost-soil water content and (2) soil water content-plant growth. We present a series of conceptual models explaining these interactions and highlight the largest sources of uncertainties. Based on these, we propose a set of hypotheses and methodologies to guide future research in this area.

Airborne particles and vapours, like many other environmental samples including water, soils and sediments, contain complex mixtures of hydrocarbons, often deriving from crude oil either before or after fractionation into fuels, lubricants and feedstocks. Comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC × GC-ToF-MS), offers a very powerful technique that separates and identifies many compounds in complicated hydrocarbon mixtures. However, quantification and identification of individual constituents at high ionization energies would require hundreds of expensive (when available) standards for calibration. Although the precise chemical structure of hydrocarbons does matter for their environmental impact and fate, strong similarities can be expected for compounds having very similar chemical structures and carbon numbers. There is, therefore, a clear benefit in an analytical technique which is specific enough to separate different classes of compounds and to distinguish homologous series while avoiding the need to handle each isomer individually. Varying EI (electron impact) ionization mass spectrometry significantly enhances the identification of individual isomers and homologous compound groups, which we refer to as “isomer sets”. Advances are reported in mapping and quantifying isomer sets of hydrocarbons (≥ C12) in diesel fuel, lubricating oil and diesel exhaust emissions. By using this analysis we report mass closures of ca. 90 and 75 % for diesel fuel and lubricating oil, and identify 85 and 75 % of the total ion current for gas- and particulate-phase diesel exhaust emissions.

Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohorts of affected individuals revealed biallelic mutations in ARHGEF18 in three such individuals. ARHGEF18 encodes ARHGEF18, a guanine nucleotide exchange factor that activates RHOA, a small GTPase protein that is a key component of tight junctions and adherens junctions. This biological pathway is known to be important for retinal development and function, as mutation of CRB1, encoding another component, causes retinal dystrophy. The retinal structure in individuals with ARHGEF18 mutations resembled that seen in subjects with CRB1 mutations. Five mutations were found on six alleles in the three individuals: c.808A>G (p.Thr270Ala), c.1617+5G>A (p.Asp540Glyfs ∗ 63), c.1996C>T (p.Arg666 ∗ ), c.2632G>T (p.Glu878 ∗ ), and c.2738_2761del (p.Arg913_Glu920del). Functional tests suggest that each disease genotype might retain some ARHGEF18 activity, such that the phenotype described here is not the consequence of nullizygosity. In particular, the p.Thr270Ala missense variant affects a highly conserved residue in the DBL homology domain, which is required for the interaction and activation of RHOA. Previously, knock-out of Arhgef18 in the medaka fish has been shown to cause larval lethality which is preceded by retinal defects that resemble those seen in zebrafish Crumbs complex knock-outs. The findings described here emphasize the peculiar sensitivity of the retina to perturbations of this pathway, which is highlighted as a target for potential therapeutic strategies.

Traffic-generated ultrafine particles (UFPs) in the urban atmosphere have a high proportion of their composition comprised of semi-volatile compounds (SVOCs). The evaporation/condensation processes of these SVOCs can alter UFP number size distributions and play an important role in determining the fate of UFPs in urban areas. The neighbourhood-scale dispersion (over distances

As evidence for the devastating impacts of air pollution on human health continues to increase, improving urban air quality has become one of the most pressing tasks facing policy makers world-wide. Increasingly, and very often on the basis of conflicting and/or weak evidence, the introduction of green infrastructure (GI) is seen as a win–win solution to urban air pollution, reducing ground-level concentrations without imposing restrictions on traffic and other polluting activities. The impact of GI on air quality is highly context dependent, with models suggesting that GI can improve urban air quality in some situations, but be ineffective or even detrimental in others. Here we set out a novel conceptual framework explaining how and where GI can improve air quality, and offer six specific policy interventions, underpinned by research, that will always allow GI to improve air quality. We call GI with unambiguous benefits for air quality GI4AQ. However, GI4AQ will always be a third-order option for mitigating air pollution, after reducing emissions and extending the distance between sources and receptors.

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.

Traffic is the key source of ultrafine particles (UFPs, particulate matter with a diameter less than 0.1 μm or 100 nm) in most urban areas. The traffic-generated UFPs vented out from an urban street mix with overlying ‘urban background air’ and are diluted whilst also undergoing change due to condensation/evaporation and other aerosol microphysics. Traffic-generated UFPs are comprised of a complex mixture of semi-volatile compounds (SVOCs) with volatility varying over many orders of magnitude, resulting in size-dependent particle composition. This study coupled the multicomponent microphysics (involving condensation/evaporation) of UFPs with the WRF v3.6.1 (Weather Research and Forecasting) large eddy simulation model (i.e. WRF-LES-UFP), and used this modelling system to investigate the general behaviour of UFPs on the neighbourhood scale (10-1000 m; transport times of few minutes) for idealised scenarios. The model captures the horizontal dispersion of UFPs downwind into the neighbourhood scale and vertical mixing with urban background air. Evaporation decreases the mode size of UFPs venting into the urban boundary layer from street-level. The neighbourhood-scale evolution of UFPs is, therefore, a combination of the effects of emissions, mixing with background, and condensation/evaporation. Total UFP number concentration and total mass concentrations scale linearly with the emission rate or the background concentration, demonstrating numerical conservation of the scheme. The linearity is less pronounced for the number concentration of smaller particles (UFP diameter less than 100 nm) with respect to UFP size and concentrations of those organic compounds with a time scale comparable to the dilution time scale (in the order of minutes), reflecting the effects (altering the particle sizes) due to condensation/evaporation.

© 2019 American Society of Human Genetics The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.

The first generation of forest free-air CO2 enrichment (FACE) experiments has successfully provided deeper understanding about how forests respond to an increasing CO2 concentration in the atmosphere. Located in aggrading stands in the temperate zone, they have provided a strong foundation for testing critical assumptions in terrestrial biosphere models that are being used to project future interactions between forest productivity and the atmosphere, despite the limited inference space of these experiments with regards to the range of global ecosystems. Now, a new generation of FACE experiments in mature forests in different biomes and over a wide range of climate space and biodiversity will significantly expand the inference space. These new experiments are: EucFACE in a mature Eucalyptus stand on highly weathered soil in subtropical Australia; AmazonFACE in a highly diverse, primary rainforest in Brazil; BIFoR-FACE in a 150-yr-old deciduous woodland stand in central England; and SwedFACE proposed in a hemiboreal, Pinus sylvestris stand in Sweden. We now have a unique opportunity to initiate a model-data interaction as an integral part of experimental design and to address a set of cross-site science questions on topics including responses of mature forests; interactions with temperature, water stress, and phosphorus limitation; and the influence of biodiversity.

A recent study demonstrated that diesel particles in urban air undergo evaporative shrinkage when advected to a cleaner atmosphere (Harrison et al., 2016). We explore, in a structured and systematic way, the sensitivity of nucleation-mode diesel particles to changes in particle composition and saturation vapour pressure. We use a multi-component aerosol microphysics model based on surrogate molecule (C16-C32 n-alkane) volatilities. For standard atmospheric conditions (298 K, 1013.25 hPa), and over timescales (ca. 100 s) relevant for dispersion on the neighbourhood scale (up to 1 km), the choice of a particular vapour pressure dataset changes the range of compounds that are appreciably volatile by 2–6 carbon numbers. The nucleation-mode peak diameter, after 100 s of model runtime, is sensitive to the vapour pressure parameterisations for particles with compositions centred on surrogate molecules between C22H46 and C24H50. The vapour pressures of components in this range are therefore critical for the modelling of nucleation-mode aerosol dynamics on the neighbourhood scale and need to be better constrained. Laboratory studies have shown this carbon number fraction to derive predominantly from engine lubricating oil. The accuracy of vapour pressure data for other (more and less volatile) components from laboratory experiments, is less critical. The influence of a core of involatile material is also considered. The new findings of this study may also be used to identify the Semi-Volatile Organic Compound (SVOC) compositions that play dominating roles in the evaporative shrinkage of the nucleation mode observed in field measurements (e.g. Dall’Osto et al., 2011). As well as reconciling model and observations, identifying the most significant vapour pressure regime for nucleation-mode dynamics offers a way to improve the computing efficiency of urban aerosol models by adopting simplified schemes for those less important components: e.g., an equilibrium scheme for low-carbon-number components and a linear scheme for high-carbon-number components.

Data and methods additional to the main manuscript

Many environmental samples, including water, soils, sediments and airborne particles and vapours contain complex mixtures of hydrocarbons, often deriving from crude oil either before or after fractionation into fuels, lubricants and feedstocks. Comprehensive 2D Gas Chromatography- Time-of-Flight Mass Spectrometry (GC &times GC-ToFMS), offers a very powerful technique separating and identifying many compounds in complicated hydrocarbon mixtures. However, quantification and identification of individual constituents at high ionization energies would require hundreds of expensive (if available) standards for calibration. Although the chemical structure of hydrocarbons does matter for their environmental impact and fate, strong similarities can be expected for compounds having very similar chemical structure and carbon number. There is, therefore, a clear benefit in an analytical technique which is specific enough to separate different classes of compounds, and to distinguish homologous series, whilst avoiding the need to handle each isomer individually. Varying EI (electron impact) ionization mass spectrometry significantly enhances the identification of individual isomers and homologous compound groups, which we refer to as isomer sets. Advances are reported in mapping and quantifying isomer sets of hydrocarbons (≥ C12) in diesel fuel, lubricating oil and diesel exhaust emissions. Using this analysis we report mass closures of ca. 90 % and 75 % for diesel fuel and lubricating oil.

This study implements a two-box model coupled with ultrafine particle (UFP) multicomponent microphysics for a compartmentalised street canyon. Canyon compartmentalisation can be described parsimoniously by three parameters relating to the features of the canyon and the atmospheric state outside the canyon, i.e. the heterogeneity coefficient, the vortex-to-vortex exchange velocity, and the box height ratio. The quasi-steady solutions for the two compartments represent a balance among emissions, microphysical aerosol dynamics (i.e. evaporation/condensation of semi-volatiles, SVOCs), and exchange processes, none of which is negligible. This coupled two-box model can capture significant contrasts in UFP number concentrations and a measure of the volatility of the multi-SVOC-particles in the lower and upper canyon. Modelled ground-level UFP number concentrations vary across nucleation, Aitken, and accumulation particle modes as well-defined monotonic functions of canyon compartmentalisation parameters. Compared with the two-box model, a classic one-box model (without canyon compartmentalisation) leads to underestimation of UFP number concentrations by several tens of percent typically. By quantifying the effects of canyon compartmentalisation, this study provides a framework for understanding how canyon geometry and the presence of street trees, street furniture, and architectural features interact with the large-scale atmospheric flow to determine ground-level pollutant concentrations., Graphical abstract Image 1, Highlights • Ultrafine particle multicomponent microphysics is coupled with a 2-box canyon model. • Significant contrasts in particle number concentrations in the canyon are captured. • Particle number concentrations vary across modes as functions of canyon parameters. • A one-box model would underestimate ground-level particle number concentrations., Effects of canyon compartmentalisation on ultrafine particle (UFP) number concentrations and volatility are revealed by the two-box model coupled with UFP multicomponent microphysics.

As part of an NERC-funded project investigating the southern methane anomaly, a team drawn from the Universities of Bristol, Birmingham and Royal Holloway flew small unmanned multirotors from Ascension Island for the purposes of atmospheric sampling. The objective of these flights was to collect air samples from below, within and above a persistent atmospheric feature, the Trade Wind Inversion, in order to characterise methane concentrations and their isotopic composition. These parameters allow the methane in the different air masses to be tied to different source locations, which can be further analysed using back trajectory atmospheric computer modelling. This paper describes the campaigns as a whole including the design of the bespoke eight rotor aircraft and the operational requirements that were needed in order to collect targeted multiple air samples up to 2.5 km above the ground level in under 20 min of flight time. Key features of the system described include real-time feedback of temperature and humidity, as well as system health data. This enabled detailed targeting of the air sampling design to be realised and planned during the flight mission on the downward leg, a capability that is invaluable in the presence of uncertainty in the pre-flight meteorological data. Environmental considerations are also outlined together with the flight plans that were created in order to rapidly fly vertical transects of the atmosphere whilst encountering changing wind conditions. Two sampling campaigns were carried out in September 2014 and July 2015 with over one hundred high altitude sampling missions. Lessons learned are given throughout, including those associated with operating in the testing environment encountered on Ascension Island.