Active site maturation and activity of the copper-radical oxidase GlxA is governed by a tryptophan residue

GlxA from Streptomyces lividans is a mononuclear copper-radical oxidase and a member of the auxiliary activity family 5 (AA5). Its domain organisation and low sequence homology make it a distinct member of the AA5 family in which the fungal galactose 6-oxidase (Gox) is the best-characterized. GlxA is a key cuproenzyme in the copper-dependent morphological development of S. lividans with a function that is linked to the processing of an extracytoplasmic glycan. The catalytic site in GlxA and Gox contain two distinct one-electron acceptors comprising the copper ion and a 3'-(S-cysteinyl) tyrosine. The latter is formed post-translationally through a covalent bond between a cysteine and a copper coordinating tyrosine ligand and houses a radical. In GlxA and Gox a second coordination sphere tryptophan residue (Trp288 in GlxA) is present, but the orientation of the indole ring differs between the two enzymes creating a marked difference in the ?-? stacking interaction of the benzyl ring with the 3'-(S-cysteinyl) tyrosine. Differences in the spectroscopic and enzymatic activity have been reported between GlxA and Gox with the indole orientation suggested as a reason. Here we report a series of in vivo and in vitro studies using the W288F and W288A variants of GlxA to assess the role of Trp288 on the morphology, maturation, spectroscopic and enzymatic properties. Our findings point towards a salient role for Trp288 in the kinetics of copper loading and maturation of GlxA, with its presence essential for stabilising the metalloradical site required for coupling catalytic activity and morphological development

Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue

Dear Editor, The bacterium Treponema pallidum (TP) causes human syphilis (subsp. pallidum; TPA), bejel (subsp. endemicum; TEN), and yaws (subsp. pertenue; TPE) (1). Although syphilis has reached a worldwide distribution (2), bejel and yaws have remained endemic diseases. Bejel affects individuals in dry areas of Sahelian Africa and Saudi Arabia, whereas yaws affects those living in the humid tropics (1). Yaws is currently reported as endemic in 14 countries, and an additional 84 countries have a known history of yaws but lack recent epidemiological data (3,4). Although this disease was subject to global eradication efforts in the mid-20th century, it later reemerged in West Africa, Southern Asia, and the Pacific region (5). New large-scale treatment options triggered the ongoing second eradication campaign, the goal of which is to eradicate yaws globally by 2020 (5). References: (1) Giacani, L. & Lukehart, S.A. The endemic treponematoses. Clin. Microbiol. Rev. 27, 89–115 (2014). (2) Arora, N. et al. Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nat. Microbiol. 2, 16245 (2016). (3) Marks, M. Yaws: towards the WHO eradication target. Trans. R Soc. Trop. Med. Hyg. 110, 319–320 (2016). (4) World Health Organization. Eradication of yaws: procedures for verification and certification of interruption of transmission (World Health Organization, Geneva, 2018). (5) Asiedu, K., Fitzpatrick, C. & Jannin, J. Eradication of yaws: historical efforts and achieving WHO’s 2020 target. PLoS Negl. Trop. Dis. 8, e3016 (2014)

Importance of proximity to resources, social support, transportation and neighborhood security for mobility and social participation in older adults: results from a scoping study

ABSTRACT: Background: Since mobility and social participation are key determinants of health and quality of life, it is important to identify factors associated with them. Although several investigations have been conducted on the neighborhood environment, mobility and social participation, there is no clear integration of the results. This study aimed to provide a comprehensive understanding regarding how the neighborhood environment is associated with mobility and social participation in older adults.Methods: A rigorous methodological scoping study framework was used to search nine databases from different fields with fifty-one keywords. Data were exhaustively analyzed, organized and synthesized according to the International Classification of Functioning, Disability and Health (ICF) by two research assistants following PRISMA guidelines, and results were validated with knowledge users.Results: The majority of the 50 selected articles report results of cross-sectional studies (29; 58 %), mainly conducted in the US (24; 48 %) or Canada (15; 30 %). Studies mostly focused on neighborhood environment associations with mobility (39; 78 %), social participation (19; 38 %), and occasionally both (11; 22 %). Neighborhood attributes considered were mainly 'Pro ducts and technology' (43; 86) and 'Services, systems and policies' (37; 74 %), but also 'Natural and human- made changes' (27; 54 %) and 'Support and relationships' (21; 42 %). Mobility and social participation were both positively associated with Proximity to resources and recreational facilities, Social support, Having a car or driver's license, Public transportation and Neighborhood security, and negatively associated with Poor user-friendliness of the walking environment and Neighborhood insecurity. Attributes of the neighborhood environment not covered by previous research on mobility and social participation mainly concerned 'Attitudes', and 'Services, systems and policies'.Conclusion: Results from this comprehensive synthesis of empirical studies on associations of the neighborhood environment with mobility and social participation will ultimately support best practices, decisions and the development of innovative inclusive public health interventions including clear guidelines for the creation of age-supportive environments. To foster mobility and social participation, these interventions must consider Proximity to resources and to recreational facilities, Social support, Transportation, Neighborhood security and User-friendliness of the walking environment. Future studies should include both mobility and social participation, and investigate how they are associated with 'Attitudes', and 'Services, systems and policies' in older adults, including disadvantaged older adults

IMPACT World+: a globally regionalized life cycle impact assessment method

Purpose This paper addresses the need for a globally regionalized method for life cycle impact assessment (LCIA), integrating multiple state-of-the-art developments as well as damages on water and carbon areas of concern within a consistent LCIA framework. This method, named IMPACT World+, is the update of the IMPACT 2002+, LUCAS, and EDIP methods. This paper first presents the IMPACT World+ novelties and results and then analyzes the spatial variability for each regionalized impact category. Methods With IMPACT World+, we propose a midpoint-damage framework with four distinct complementary viewpoints to present an LCIA profile: (1) midpoint impacts, (2) damage impacts, (3) damages on human health, ecosystem quality, and resources & ecosystem service areas of protection, and (4) damages on water and carbon areas of concerns. Most of the regional impact categories have been spatially resolved and all the long-term impact categories have been subdivided between shorterterm damages (over the 100 years after the emission) and long-term damages. The IMPACT World+ method integrates developments in the following categories, all structured according to fate (or competition/scarcity), exposure, exposure response, and severity: (a) Complementary to the global warming potential (GWP100), the IPCC Global Temperature Potentials (GTP100) are used as a proxy for climate change long-term impacts at midpoint. At damage level, shorter-term damages (over the first 100 years after emission) are also differentiated from long-term damages. (b) Marine acidification impact is based on the same fate model as climate change, combined with the H+ concentration affecting 50% of the exposed species. (c) For mineral resources depletion impact, the material competition scarcity index is applied as a midpoint indicator. (d) Terrestrial and freshwater acidification impact assessment combines, at a resolution of 2° × 2.5° (latitude × longitude), global atmospheric source-deposition relationships with soil and water ecosystems’sensitivity. (e) Freshwater eutrophication impact is spatially assessed at a resolution grid of 0.5° × 0.5°, based on a global hydrological dataset. (f) Ecotoxicity and human toxicity impact are based on the parameterized version of USEtox for continents. We consider indoor emissions and differentiate the impacts of metals and persistent organic pollutants for the first 100 years from longer-term impacts. (g) Impacts on human health related to particulate matter formation are modeled using the USEtox regional archetypes to calculate intake fractions and epidemiologically derived exposure response factors. (h) Water consumption impacts are modeled using the consensus-based scarcity indicator AWARE as a proxy midpoint, whereas damages account for competition and adaptation capacity. (i) Impacts on ecosystem quality from land transformation and occupation are empirically characterized at the biome level. Results and discussion We analyze the magnitude of global potential damages for each impact indicator, based on an estimation of the total annual anthropogenic emissions and extractions at the global scale (i.e., Bdoing the LCA of the world^). Similarly with ReCiPe and IMPACT 2002+, IMPACT World+ finds that (a) climate change and impacts of particulate matter formation have a dominant contribution to global human health impacts whereas ionizing radiation, ozone layer depletion, and photochemical oxidant formation have a low contribution and (b) climate change and land use have a dominant contribution to global ecosystem quality impact. (c) New impact indicators introduced in IMPACT World+ and not considered in ReCiPe or IMPACT 2002+, in particular water consumption impacts on human health and the long-term impacts of marine acidification on ecosystem quality, are significant contributors to the overall global potential damage. According to the areas of concern version of IMPACT World+ applied to the total annual world emissions and extractions, damages on the water area of concern, carbon area of concern, and the remaining damages (not considered in those two areas of concern) are of the same order of magnitude, highlighting the need to consider all the impact categories. The spatial variability of human health impacts related to exposure to toxic substances and particulate matter is well reflected by using outdoor rural, outdoor urban, and indoor environment archetypes. For Bhuman toxicity cancer^ impact of substances emitted to continental air, the variability between continents is of two orders of magnitude, which is substantially lower than the 13 orders of magnitude total variability across substances. For impacts of water consumption on human health, the spatial variability across extraction locations is substantially higher than the variations between different water qualities. For regionalized impact categories affecting ecosystem quality (acidification, eutrophication, and land use), the characterization factors of half of the regions (25th to 75th percentiles) are within one to two orders of magnitude and the 95th percentile within three to four orders of magnitude, which is higher than the variability between substances, highlighting the relevance of regionalizing. Conclusions IMPACT World+ provides characterization factors within a consistent impact assessment framework for all regionalized impacts at four complementary resolutions: global default, continental, country, and native (i.e., original and non-aggregated) resolutions. IMPACT World+ enables the practitioner to parsimoniously account for spatial variability and to identify the elementary flows to be regionalized in priority to increase the discriminating power of LCA

Global guidance on environmental life cycle impact assessment indicators: Progress and case study

International audiencePurpose: The life cycle impact assessment (LCIA) guidance flagship project of the United Nations Environment Programme (UNEP)/Society of Environmental Toxicology and Chemistry (SETAC) Life Cycle Initiative aims at providing global guidance and building scientific consensus on environmental LCIA indicators. This paper presents the progress made since 2013, preliminary results obtained for each impact category and the description of a rice life cycle assessment (LCA) case study designed to test and compare LCIA indicators. Methods: The effort has been focused in a first stage on impacts of global warming, fine particulate matter emissions, water use and land use, plus cross-cutting issues and LCA-based footprints. The paper reports the process and progress and specific results obtained in the different task forces (TFs). Additionally, a rice LCA case study common to all TF has been developed. Three distinctly different scenarios of producing and cooking rice have been defined and underlined with life cycle inventory data. These LCAs help testing impact category indicators which are being developed and/or selected in the harmonisation process. The rice LCA case study further helps to ensure the practicality of the finally recommended impact category indicators. Results and discussion: The global warming TF concludes that analysts should explore the sensitivity of LCA results to metrics other than GWP. The particulate matter TF attained initial guidance of how to include health effects from PM2.5 exposures consistently into LCIA. The biodiversity impacts of land use TF suggests to consider complementary metrics besides species richness for assessing biodiversity loss. The water use TF is evaluating two stress-based metrics, AWaRe and an alternative indicator by a stakeholder consultation. The cross-cutting issues TF agreed upon maintaining disability-adjusted life years (DALY) as endpoint unit for the safeguard subject 'human health'. The footprint TF defined main attributes that should characterise all footprint indicators. 'Rice cultivation' and 'cooking' stages of the rice LCA case study contribute most to the environmental impacts assessed. Conclusions: The results of the TF will be documented in white papers and some published in scientific journals. These white papers represent the input for the Pellston workshop', taking place in Valencia, Spain, from 24 to 29 January 2016, where best practice, harmonised LCIA indicators and an update on the general LCIA framework will be discussed and agreed on. With the diversity in results and the multi-tier supply chains, the rice LCA case study is well suited to test candidate recommended indicators and to ensure their applicability in common LCA case studies

Variation in carbon and nitrogen concentrations among peatland categories at the global scale

Publisher Copyright: © 2022 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.Peer reviewe

Making sense of the minefield of footprint indicators

In recent years, footprint indicators have emerged as a popular mode of reporting environmental performance. The prospect is that these simplified metrics will guide investors, businesses, public sector policymakers and even consumers of everyday goods and services in making decisions which lead to better environmental outcomes. However, without a common “DNA”, the ever expanding lexicon of footprints lacks coherence and may even report contradictory results for the same subject matter.(1) The danger is that this will ultimately lead to policy confusion and general mistrust of all environmental disclosures. Footprints are especially interesting metrics because they seek to express the environmental performance of products and organizations from a life cycle perspective. The life cycle perspective is important to avoid misleading claims based only on a selected life cycle stage. For example, the water used to manufacture beverages may be important, but if a beverage includes sugar, irrigation water used to cultivate sugar cane could be a greater concern. The focus on environmental performance distinguishes footprints from technical efficiency measures, such as energy use efficiency or water use efficiency, which typically only make sense when applied to a single life cycle stage as they lack local environmental context. However, unlike technical efficiency, which can usually be accurately measured and verified, footprint indicators, with their wider view of environmental performance, are usually calculated using models which can differ in scope, complexity and model parameter settings. Despite the noble intention of using footprints to evaluate and report environmental performance, the potential inconsistency between different approaches acts as a deterrent to use in many public policymaking and business contexts and can lead to confusing and contradictory messages in the marketplace

Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

Background: Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi. Results: We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc. Conclusions: This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content