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Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. Results In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. Availability and implementation UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.

Open-water perennial pools are common natural features of peatlands globally, and peatland restoration often results in new pool creation, yet the concentrations of different forms of aquatic carbon (C) in natural and artificial restoration pools are not well studied. We compared carbon concentrations in both natural pools and restoration pools (4–15 years old) on three blanket peatlands in northern Scotland. At all sites, restoration pools were more acidic and had mean dissolved organic carbon (DOC) concentrations in restoration pools of 23, 22, and 31 mg L−1 compared with natural pool means of 11, 11 and 15 mg L−1 respectively across the three sites. Restoration pools had a greater fulvic acid prevalence than the natural pools and their DOC was more aromatic. Restoration pools were supersaturated with dissolved CO2 at around 10 times atmospheric levels, whereas for natural pools, CO2 concentrations were just above atmospheric levels. Dissolved CH4 concentrations were not different between pool types, but were ~200 times higher than atmospheric levels. Regular sampling at one of the peatland sites over 2.5 years showed that particulate organic carbon (POC) concentrations were generally below 7 mg L−1 except during the warm, dry summer of 2013. At this regularly-sampled site, natural pools were found to process DOC so that mean pool outflow concentrations in overland flow were significantly lower than mean inflow DOC concentrations. Such an effect was not found for the restoration pools. Soil solution and pool water chemistry, and relationships between DOC and CO2 concentrations suggest that different processes are controlling the transformation of C, and therefore the form and amount of C, in natural pools compared to restoration pools.

During the 1980s, Ronald and Nancy Reagan served as dual figureheads in the United States’ War on Drugs. While the policies and impacts of that campaign have been documented extensively by scholars, this project addresses the cultural side of the anti-drug movement which was crucial for gaining consent for the drug war’s broader policy goals. During both terms of the Reagan administration, celebrities, athletes, and entertainment industry executives were responsible for producing hundreds of public service announcements, rallies, and other media campaigns, some of which were created directly in collaboration with government officials and some of which were created independently. All of those public service announcements and media campaigns served as key sites wherein the state defined the stakes of the drug crisis and sold the public on its vision for the broader anti-drug effort. The messages put forth by athletes and entertainers through their own platforms or in collaboration with Nancy Reagan’s “Just Say No” campaign directly reflected the Reagan administration’s political and cultural perspectives and helped reify the moral panic that underpinned those perspectives. Celebrity-backed campaigns especially reinforced the ideas that the drug war was to be fought voluntarily by individuals and non-governmental organizations, and that drug abuse could be made culturally unacceptable and thus prevented by framing drug users as irresponsible members of society. The cultural side of the anti-drug movement reflected the deeply racialized dimensions of the broader War on Drugs – especially after the ascent of the crack cocaine epidemic – where the political and media framing of crack as a “Black drug” prompted the creation of anti-drug messaging that featured Black celebrities and that was targeted at young Black Americans.

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

The carbon sink potential of peatlands depends on the balance of carbon uptake by plants and microbial decomposition. The rates of both these processes will increase with warming but it remains unclear which will dominate the global peatland response. Here we examine the global relationship between peatland carbon accumulation rates during the last millennium and planetary-scale climate space. A positive relationship is found between carbon accumulation and cumulative photosynthetically active radiation during the growing season for mid- to high-latitude peatlands in both hemispheres. However, this relationship reverses at lower latitudes, suggesting that carbon accumulation is lower under the warmest climate regimes. Projections under Representative Concentration Pathway (RCP)2.6 and RCP8.5 scenarios indicate that the present-day global sink will increase slightly until around AD 2100 but decline thereafter. Peatlands will remain a carbon sink in the future, but their response to warming switches from a negative to a positive climate feedback (decreased carbon sink with warming) at the end of the twenty-first century.

High-resolution analyses of plant macrofossils, testate amoebae, pollen, mineral content, bulk density, and carbon and nitrogen were undertaken to examine the late Holocene dynamics of two permafrost peatlands in Abisko, Subarctic Sweden. The peat records were dated using tephrochronology, 14C and 210Pb. Local plant succession and hydrological changes in peatlands were synchronous with climatic shifts, although autogenous plant succession towards ombrotrophic status during peatland development was also apparent. The Marooned peatland experienced a shift ca. 2250 cal yr BP from rich to poor fen, as indicated by the appearance of Sphagnum fuscum. At Stordalen, a major shift to wetter conditions occurred between 500 and 250 cal yr BP, probably associated with climate change during the Little Ice Age. During the last few decades, the testate amoeba data suggest a deepening of the water table and an increase in shrub pollen, coinciding with recent climate warming and the associated expansion of shrub communities across the Arctic. Rates of carbon accumulation vary greatly between the sites, illustrating the importance of local vegetation communities, hydrology and permafrost dynamics. Multiproxy data elucidate the palaeoecology of S. lindbergii and show that it indicates wet conditions in peatlands. Copyright © 2017 John Wiley & Sons, Ltd.

Climate warming and human impacts are thought to be causing peatlands to dry,\ud potentially converting them from sinks to sources of carbon. However, it is unclear\ud whether the hydrological status of peatlands has moved beyond their natural envelope.\ud Here we show that European peatlands have undergone substantial, widespread drying\ud during the last ~300 years. We analyse testate amoeba-derived hydrological\ud reconstructions from 31 peatlands across Britain, Ireland, Scandinavia and continental\ud Europe to examine changes in peatland surface wetness during the last 2000 years.\ud 60% of our study sites were drier during the period CE 1800-2000 than they have been\ud for the last 600 years; 40% of sites were drier than they have been for 1000 years; and\ud 24% of sites were drier than they have been for 2000 years. This marked recent\ud transition in the hydrology of European peatlands is concurrent with compound\ud pressures including climatic drying, warming and direct human impacts on peatlands,\ud although these factors vary between regions and individual sites. Our results suggest\ud that the wetness of many European peatlands may now be moving away from natural\ud baselines. Our findings highlight the need for effective management and restoration of\ud European peatlands.

UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute to this process with a FAIRness assessment of our UniProtKB dataset followed by a critical reflection on the challenges and future directions of the adoption and validation of the FAIR principles and metrics.

Summary Many peatland ecosystems in Europe have become degraded in the last century owing to the effects of drainage, burning, pollution and climate change. There is a need to understand the drivers of peatland degradation because management and restoration interventions are expensive and can affect the natural ecohydrological dynamics of such sensitive environments. However, if given enough time, peatlands may have the ability to recover spontaneously without deliberate action. We use a detailed multiproxy palaeoecological data set from a degraded raised bog in Northern England to examine its ecosystem stability and long-term dynamics in response to anthropogenic disturbance over a variety of timescales. One feature of many degraded peatlands (including our study site) is the local dominance of Molinia caerulea (purple moor-grass), which has expanded at the expense of characteristic peatland plants, including sedges and Sphagnum mosses. Our data show that there has been a long history of human impacts at the site which have culminated in its current unfavourable condition. Several distinct episodes of past peat cutting are evident as hiatuses in peat accumulation; however, peat accumulation and plant community structure have subsequently recovered spontaneously. The appearance of M. caerulea occurs coevally with an unprecedented variety of recent anthropogenic impacts, all of which have contributed to providing a suitable environment for its rise to dominance. We have dated the appearance of M. caerulea to the latter half of the twentieth century which corresponds to a number of anthropogenic press disturbances, including the following: dust loading from post-war expansion of the adjacent quarry; burning; drainage; airborne pollution; and contamination from soil dust and agrochemicals. [Synthesis] Our study demonstrates the importance of palaeoecology for understanding the trajectories of peatland development and ecosystem dynamics, including their resilience and resistance to pulse and press disturbances. We show that peatlands have the capability to recover spontaneously from severe disturbances such as peat cutting, albeit on timescales much longer than those applied to contemporary monitoring of restoration efforts. The implications are relevant for determining whether it is preferable to manage and restore peatlands, or to allow them to recover naturally without human intervention.

Ombrotrophic peatlands have provided important archives for understanding Holocene palaeoenvironmental change. However, records are predominantly from raised bogs due to potential issues regarding preservation of proxy indicators, record length and low temporal resolution in other peat types including blanket bogs. By carrying out peat depth and stratigraphy surveys we demonstrate how blanket peatlands can provide archives capable of providing records that are not reliant on single proxies, as has been often the case in the past, and can provide good resolution records. A record containing humification, testate amoebae and plant macrofossils was derived for the last 3000 years with accumulation rates as high as 8 yrs cm− 1 providing favourable temporal resolution, particularly over the last 1500 years. Major changes in proxy indicators reflecting potential changes in water-table depth were often coherent with changes in climate. Human activity also had a major impact on the peatland throughout the record especially in the last 100 years where the influence of wildfire and managed burning, together with an effect of atmospheric pollution, fundamentally changed the state of the peatland.

Perennial pools are common natural features of peatlands, and their hydrological functioning and turnover may be important for carbon fluxes, aquatic ecology, and downstream water quality. Peatland restoration methods such as ditch blocking result in many new pools. However, little is known about the hydrological function of either pool type. We monitored six natural and six artificial pools on a Scottish blanket peatland. Pool water levels were more variable in all seasons in artificial pools having greater water level increases and faster recession responses to storms than natural pools. Pools overflowed by a median of 9 and 54 times pool volume per year for natural and artificial pools, respectively, but this varied widely because some large pools had small upslope catchments and vice versa. Mean peat water-table depths were similar between natural and artificial pool sites but much more variable over time at the artificial pool site, possibly due to a lower bulk specific yield across this site. Pool levels and pool-level fluctuations were not the same as those of local water tables in the adjacent peat. Pool-level time series were much smoother, with more damped rainfall or recession responses than those for peat water tables. There were strong hydraulic gradients between the peat and pools, with absolute water tables often being 20–30 cm higher or lower than water levels in pools only 1–4 m away. However, as peat hydraulic conductivity was very low (median of 1.5 × 10−5 and 1.4 × 10−6 cm s−1 at 30 and 50 cm depths at the natural pool site), there was little deep subsurface flow interaction. We conclude that (a) for peat restoration projects, a larger total pool surface area is likely to result in smaller flood peaks downstream, at least during summer months, because peatland bulk specific yield will be greater; and (b) surface and near-surface connectivity during storm events and topographic context, rather than pool size alone, must be taken into account in future peatland pool and stream chemistry studies.