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Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples., Competing Interests: Authors declare no conflicts of interests., (Copyright © 2024 The Authors.)

Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.

Pollen and tracheophyte spores are ubiquitous environmental indicators at local and global scales. Palynology is typically performed manually by microscopic analysis; a specialised and time-consuming task limited in taxonomical precision and sampling frequency, therefore restricting data quality used to inform climate change and pollen forecasting models. We build on the growing work using AI (artificial intelligence) for automated pollen classification to design a flexible network that can deal with the uncertainty of broad-scale environmental applications. We combined imaging flow cytometry with Guided Deep Learning to identify and accurately categorise pollen in environmental samples; here, pollen grains captured within c. 5500 Cal yr BP old lake sediments. Our network discriminates not only pollen included in training libraries to the species level but, depending on the sample, can classify previously unseen pollen to the likely phylogenetic order, family and even genus. Our approach offers valuable insights into the development of a widely transferable, rapid and accurate exploratory tool for pollen classification in 'real-world' environmental samples with improved accuracy over pure deep learning techniques. This work has the potential to revolutionise many aspects of palynology, allowing a more detailed spatial and temporal understanding of pollen in the environment with improved taxonomical resolution., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

Atmospheric particulate matter (PM) causes 3.7 million annual deaths worldwide and potentially damages every organ in the body. The cancer-causing potential of fine particulates (PM 2.5 ) highlights the inextricable link between air quality and human health. With over half of the world's population living in cities, PM 2.5 emissions are a major concern, however, our understanding of exposure to urban PM is restricted to relatively recent (post-1990) air quality monitoring programmes. To investigate how the composition and toxicity of PM has varied within an urban region, over timescales encompassing changing patterns of industrialisation and urbanisation, we reconstructed air pollution records spanning 200 years from the sediments of urban ponds in Merseyside (NW England), a heartland of urbanisation since the Industrial Revolution. These archives of urban environmental change across the region demonstrate a key shift in PM emissions from coarse carbonaceous 'soot' that peaked during the mid-twentieth century, to finer combustion-derived PM 2.5 post-1980, mirroring changes in urban infrastructure. The evolution of urban pollution to a recent enhanced PM 2.5 signal has important implications for understanding lifetime pollution exposures for urban populations over generational timescales., (© 2023. The Author(s).)

The sediment microbiome is a demographically diverse and functionally active biosphere. Ensuring that data acquired from sediment is truly representative of the microbiome is critical to achieving robust analyses. Sample storage and the processing and timing of nucleic acid purification after environmental sample extraction may fundamentally affect the detectable microbial community and thereby significantly alter resultant data. Direct sequencing of environmental samples is increasingly commonplace due to the advent of the portable Oxford Nanopore MinION sequencing device. Here we demonstrate that storing sediment subsamples at - 20 °C or storing the cores at 4 °C for 10 weeks prior to analysis, has a significant effect on the sediment microbiome analysed using sedimentary DNA (sedDNA), especially for Alpha-, Beta- and Deltaproteobacteria species. Furthermore, these significant differences are observed regardless of sediment type. We show that the taxa which are predominantly affected by storage are Proteobacteria, and therefore recommend on-site purifications are performed to ensure an accurate representation of these taxa are observed in the microbiome. Comparisons of sedimentary RNA (sedRNA) analyses, revealed substantial differences between samples purified and sequenced immediately on-site, samples that were frozen before transportation, and cores that were stored at 4 °C prior to analysis. Our data therefore suggest that a more accurate representation of the sediment microbiome demography and functionality may be achieved by environmental sequencing as rapidly as possible to minimise confounding effects of storage., (© 2022. The Author(s).)

Weissella paramesenteroides has potential as an industrial biocatalyst due to its ability to produce lactic acid. A novel strain of W. paramesenteroides was isolated from ensiled sorghum. The genome was sequenced using a hybrid assembly of Oxford Nanopore and Illumina data to produce a 2-Mbp genome and 22-kbp plasmid sequence., (Copyright © 2021 Baugh et al.)

The viable but non culturable (VBNC) state is a condition in which bacterial cells are viable and metabolically active, but resistant to cultivation using a routine growth medium. We investigated the ability of V. parahaemolyticus to form VBNC cells, and to subsequently become resuscitated. The ability to control VBNC cell formation in the laboratory allowed us to selectively isolate VBNC cells using fluorescence activated cell sorting, and to differentiate subpopulations based on their metabolic activity, cell shape and the ability to cause disease in Galleria mellonella. Our results showed that two subpopulations (P1 and P2) of V. parahaemolyticus VBNC cells exist and can remain dormant in the VBNC state for long periods. VBNC subpopulation P2, had a better fitness for survival under stressful conditions and showed 100% revival under favourable conditions. Proteomic analysis of these subpopulations (at two different time points: 12 days (T12) and 50 days (T50) post VBNC) revealed that the proteome of P2 was more similar to that of the starting microcosm culture (T0) than the proteome of P1. Proteins that were significantly up or down-regulated between the different VBNC populations were identified and differentially regulated proteins were assigned into 23 functional groups, the majority being assigned to metabolism functional categories. A lactate dehydrogenase (lldD) protein, responsible for converting lactate to pyruvate, was significantly upregulated in all subpopulations of VBNC cells. Deletion of the lactate dehydrogenase (RIMD2210633:ΔlldD) gene caused cells to enter the VBNC state significantly more quickly compared to the wild-type, and adding lactate to VBNC cells aided their resuscitation and extended the resuscitation window. Addition of pyruvate to the RIMD2210633:ΔlldD strain restored the wild-type VBNC formation profile. This study suggests that lactate dehydrogenase may play a role in regulating the VBNC state., Competing Interests: The authors have declared that no competing interests exist.

The formation of persister cells is one mechanism by which bacteria can survive exposure to environmental stresses. We show that Campylobacter jejuni 11168H forms persister cells at a frequency of 10 -3 after exposure to 100 × MIC of penicillin G for 24 h. Staining the cell population with a redox sensitive fluorescent dye revealed that penicillin G treatment resulted in the appearance of a population of cells with increased fluorescence. We present evidence, to show this could be a consequence of increased redox protein activity in, or associated with, the electron transport chain. These data suggest that a population of penicillin G treated C. jejuni cells could undergo a remodeling of the electron transport chain in order to moderate membrane hyperpolarization and intracellular alkalization; thus reducing the antibiotic efficacy and potentially assisting in persister cell formation., (Copyright © 2020 Morcrette, Kovacs-Simon, Tennant, Love, Wagley, Yang, Studholme, Soyer, Champion, Butler and Titball.)

Designing improved vaccines against mutable viruses such as dengue and influenza would be helped by a better understanding of how the B-cell memory compartment responds to variant antigens. Towards this we have recently shown, after secondary immunization of mice with a widely variant dengue virus envelope protein with only 63% amino acid identity, that IgM + memory B cells with few mutations supported an efficient secondary germinal centre (GC) and serum response, superior to a primary response to the same protein. Here, further investigation of memory responses to variant proteins, using more closely related influenza virus haemagglutinins (HA) that were 82% identical, produced a variant-induced boost response in the GC dominated by highly mutated B cells that failed, not efficiently improving serum avidity even in the presence of extra adjuvant, and that was worse than a primary response. This supports a hypothesis that over a certain level of antigenic differences, cross-reactive memory B-cell populations have reduced competency for affinity maturation. Combined with our previous observations, these findings also provide new parameters of success and failure in antibody memory responses., (© 2019 The Authors. Immunology Published by John Wiley & Sons Ltd.)

Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.

Thermoanaerobacter ethanolicus JW 200 has been identified as a potential sustainable biofuel producer due to its ability to readily ferment carbohydrates to ethanol. A hybrid sequencing approach, combining Oxford Nanopore and Illumina DNA sequence reads, was applied to produce a single contiguous genome sequence of 2,911,280 bp.

Vaccines induce memory B-cells that provide high affinity secondary antibody responses to identical antigens. Memory B-cells can also re-instigate affinity maturation, but how this happens against antigenic variants is poorly understood despite its potential impact on driving broadly protective immunity against pathogens such as Influenza and Dengue. We immunised mice sequentially with identical or variant Dengue-virus envelope proteins and analysed antibody and germinal-centre (GC) responses. Variant protein boosts induced GCs with a higher proportion of IgM+ B cells. The most variant protein re-stimulated GCs with the highest proportion of IgM+ cells with the most diverse, least mutated V-genes and with a slower but efficient serum antibody response. Recombinant antibodies from GC B-cells showed a higher affinity for the variant antigen than antibodies from a primary response, confirming a memory origin. This reveals a new process of antibody memory, that IgM memory cells with fewer mutations participate in secondary responses to variant antigens, demonstrating how the hierarchical structure of B-cell memory is used and indicating the potential and limits of cross-reactive antibody based immunity., Competing Interests: BB, RT, JL, RT, DW, HW No competing interests declared, (© 2018, Burton et al.)

The colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that are mainly distinguished by the hydrocarbons produced. We previously reported a B race draft nuclear genome, and here we report the draft nuclear genomes for the A and L races. A comparative genomic study of the three B. braunii races and 14 other algal species within Chlorophyta revealed significant differences in the genomes of each race of B. braunii. Phylogenomically, there was a clear divergence of the three races with the A race diverging earlier than both the B and L races, and the B and L races diverging from a later common ancestor not shared by the A race. DNA repeat content analysis suggested the B race had more repeat content than the A or L races. Orthogroup analysis revealed the B. braunii races displayed more gene orthogroup diversity than three closely related Chlamydomonas species, with nearly 24-36% of all genes in each B. braunii race being specific to each race. This analysis suggests the three races are distinct species based on sufficient differences in their respective genomes. We propose reclassification of the three chemical races to the following species names: Botryococcus alkenealis (A race), Botryococcus braunii (B race), and Botryococcus lycopadienor (L race). [ABSTRACT FROM AUTHOR]

Chronic wounds are reoccurring healthcare problems in the United States and cost up to $50 billion annually. Improper wound care results in complications such as wound debridement, surgical amputation, and increased morbidity/ mortality due to opportunistic infections. To eliminate wound infections, many antimicrobial dressings are developed and submitted to FDA for evaluation. AATCC-100 is a standard method widely used to evaluate cloth wound dressings. This method, requires enrichment, followed by culturing to measure the concentration of culturable organisms; a caveat to this method could result in neglected viable but nonculturable (VBNC) bacteria and overestimate the antimicrobial properties of wound dressings. Therefore, the objectives of this study were to assess this accepted protocol with quantitative real-time polymerase chain reaction (qRT-PCR), to measure time dependent antimicrobial efficacy of wound dressing, and to examine for potential viable bacteria but non-culturable as compared with traditional plating methods. The test organisms included opportunistic pathogens: Pseudomonas aeruginosa (ATCC 15692) and Staphylococcus aureus (ATCC 43300). To mimic a wound dressing environment, samples of commercially available wound dressings (McKesson Inc.) with silver ion (positive control) and dressings without silver ion (positive control) were assessed under sterile conditions. All samples were examined by the original protocol (the extended AATCC-100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P. aeruginosa and 16s rRNA for S. aureus). Based on these tests, log reduction of experimental conditions was compared to identify time dependent and precise antimicrobial properties from wound dressing samples. These results showed antimicrobial properties of wound dressings diminished as incubation days are increased for both methods from day 1 PCR result of 4.31 ± 0.54 and day 1 plating result of 6.31 ± 3.04 to day 3 PCR result of 1.22 ± 0.97 and day 3 plating result of 5.89 ± 2.41. These results show that data from qRT-PCR generally produced lower standard deviation than that of culture methods, hence shown to be more precise. Complementary parallel analysis of samples using both methods better characterized antimicrobial properties of the tested samples. [ABSTRACT FROM AUTHOR]

Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings. [ABSTRACT FROM AUTHOR]

Automated pollen analysis is not yet efficient on environmental samples containing many pollen taxa and debris, which are typical in most pollen-based studies. Contrary to classification, detection remains overlooked although it is the first step from which errors can propagate. Here, we investigated a simple but efficient method to automate pollen detection for environmental samples, optimizing workload and performance. We applied the YOLOv5 algorithm on samples containing debris and c. 40 Mediterranean plant taxa, designed and tested several strategies for annotation, and analyzed variation in detection errors. About 5% of pollen grains were left undetected, while 5% of debris were falsely detected as pollen. Undetected pollen was mainly in poor-quality images, or of rare and irregular morphology. Pollen detection remained effective when applied to samples never seen by the algorithm, and was not improved by spending time to provide taxonomic details. Pollen detection of a single model taxon reduced annotation workload, but was only efficient for morphologically differentiated taxa. We offer guidelines to plant scientists to analyze automatically any pollen sample, providing sound criteria to apply for detection while using common and user-friendly tools. Our method contributes to enhance the efficiency and replicability of pollen-based studies., (© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.)

Background: The purpose of this research is to study the contribution of epiphytic microbiota in fresh oat (OT), Italian ryegrass (IR) and whole-crop maize (MZ) to silage fermentation products and bacterial community structure of MZ. After γ-ray irradiation, the sterile MZ was treated via microbiota transplantation method: (1) sterile deionized water (STMZ); (2) microbiota epiphytic on MZ (MZMZ); (3) microbiota epiphytic on OT (MZOT); (4) microbiota epiphytic on IR (MZIR). Triplicate silos of each treatment were tested after 1, 3, 7, 15, 30 and 60 days of ensiling. Results: MZMZ had higher (P < 0.05) lactic acid contents, and lower (P < 0.05) ammonia nitrogen and ethanol contents than MZIR and MZOT on day 60. The relative abundance of Lactobacillus in MZMZ decreased from 84.0% on day 3 to 44.7% on day 60. MZMZ had higher (P < 0.05) abundances of 'Nucleotide metabolism', 'Replication and repair' and 'Membrane transport', and lower (P < 0.05) abundance of 'Amino acid metabolism' than MZOT and MZIR on day 3. Conclusions: The silage fermentation products of MZ were highly affected by the activity and compositions of epiphytic microbiota. The Enterobacteriaceae, Hafnia-Obesumbacterium, hetero-fermentative and acid-resistant Lactobacillus took primary responsibility for the high dry matter loss and ethanol contents and low lactic acid contents in MZ silage. [ABSTRACT FROM AUTHOR]

Patients with SLE are at high risk of various infections as evidenced by a number of studies. The main determinants of infection in SLE are disease activity, organ damage, and often inevitable medication. The molecular and cellular mechanisms underlying infection remain unclear. Impaired immunity, immunosuppressants and corticosteroids clearly increase the risk of infection, whereas some medications, such as low-dose IL-2, hydroxychloroquine and IVIG are safe in SLE patients with substantial evidence. It is important to balance the immunosuppression and infection risks in practice. This article focuses on medication-related infections in SLE and discusses the therapeutic options for the disease in clinical practice. [ABSTRACT FROM AUTHOR]

It is necessary to purify diatom frustules by taxon to perform accurate geochemical analyses of diatom fossils preserved in sediments. However, the small size of diatoms has hitherto prevented taxon-specific purification; therefore, previous geochemical analyses of diatom frustules have been performed with mixtures of various taxa. In this study, we developed a taxon-selective collection method of diatom fossils that uses a cell sorter. The experimental material comprised six samples from a sediment core of Hole U1538A in the Scotia Sea, Atlantic sector of the Southern Ocean drilled during the International Ocean Discovery Program Expedition 382. Following conventional pretreatments (removal of organic matter and carbonates as well as clay minerals), we conducted cell sorter experiments focusing on the optical and fluorescence characteristics of the diatom fossils. We succeeded in selectively isolating with high purity five diatom taxa representing the Southern Ocean diatom flora: (1) discoid diatoms (mainly Thalassiosira) with a moderate degree of fluorescence; (2) Fragilariopsis (mainly Fragilariopsis kerguelensis), which exhibits the highest fluorescence values; (3) Rhizosolenia; (4) Eucampia antarctica; and (5) needle-shaped diatoms (Thalassiothrix). This taxon-specific diatom purification method will enable more accurate geochemical analyses, such as the oxygen isotope ratio (δ18O) of diatom frustules, which is likely to lead to significant advances in paleoceanography, especially at high latitudes or in upwelling zones where diatoms are abundant. This method will also be useful in paleolimnology, ocean biology, and phycology. [ABSTRACT FROM AUTHOR]

Purpose: Aquatic bacteria of the genus Vibrio include animal and human pathogens. The occurrence of Vibrio-related diseases has been associated with the current climate change-driven increase of sea surface temperature. Vibrio spp. can enter into the viable but non-culturable (VBNC) state, as a consequence of starvation in seawater at low temperatures. In such physiological state, Vibrio cells are no longer culturable on standard media agar plates but can resuscitate if incubated at 30 °C prior to plating, retaining virulence. Since limited information is available on regards to this topic, in this work, we characterized the phenotypic changes of four Vibrio spp. strains (one laboratory strain and three environmental isolates) in cold seawater microcosms, investigating the relationship between resuscitation and a hydrogen peroxide-induced oxidative stress. Methods: Cell phenotypic changes and the effect of hydrogen peroxide and/or catalase addition to the medium were studied on VBNC and resuscitated cells by flow cytometry in microcosm experiments, paralleled by culturability experiments by plating. Results: The cells of all the Vibrio strains changed their phenotype upon the induction of the VBNC state resulting in cell dwarfing and decrease in DNA quantity, losing the ability to grow on solid media. These features were partially or totally reverted when the cells were treated for resuscitation. Hydrogen peroxide at concentrations as low as 0.007 mM prevented resuscitation and a prolonged exposure to hydrogen peroxide at concentrations far under those inhibiting the growth of log-phase cells permanently damaged VBNC cells, which could not be resuscitated. However, the potential of culturability of VBNC cells could be preserved, at least for a part of the population, by plating the cells in the presence of catalase. The study also showed that during the resuscitation process, the cells gradually increased their resistance to hydrogen peroxide. Conclusions: The timing and mode of induction of the VBNC state, as well as cell resuscitation and response to hydrogen peroxide, differed among Vibrio strains, indicating that induction and resuscitation from dormancy could vary in the context of species belonging to a single genus. [ABSTRACT FROM AUTHOR]

Ambient air quality of Rajkot city is analyzed along with chemical characterization such as anions, cations, metals and non-sea salts (nss) to understand the chemical footprints on a regional scale. Two sites, rural and urban areaare selected for sampling of PM10,PM2.5,SO2 and NO2, but no major differences are found in ambient air quality.The concentration of ions is found to be high during summer and winter, that is, months of May and December. The concentration of anions and cations in chronological order is Cl−42−2−< NO3−3⁻−and NH4+2+++2+. Similarly, the metal concentration follows the order Na

Green infrastructure plays a vital role in urban ecosystems. This includes sustaining biodiversity and human health. Despite a large number of studies investigating greenspace disparities in suburban areas, no known studies have compared the green attributes (e.g., trees, greenness, and greenspaces) of urban centres. Consequently, there may be uncharacterised socioecological disparities between the cores of urban areas (e.g., city centres). This is important because people spend considerable time in urban centres due to employment, retail and leisure opportunities. Therefore, the availability of––and disparities in––green infrastructure in urban centres can affect many lives and potentially underscore a socio-ecological justice issue. To facilitate comparisons between urban centres in Great Britain, we analysed open data of urban centre boundaries with a central business district and population of ≥100,000 (n = 68). Given the various elements that contribute to 'greenness', we combine a range of different measurements (trees, greenness, and accessible greenspaces) into a single indicator. We applied the normalised difference vegetation index (NDVI) to estimate the mean greenness of urban centres and the wider urban area (using a 1 km buffer) and determined the proportion of publicly accessible greenspace within each urban centre with Ordnance Survey Open Greenspace data. Finally, we applied a land cover classification algorithm using i-Tree Canopy to estimate tree coverage. This is the first study to define and rank urban centres based on multiple green attributes. The results suggest important differences in the proportion of green attributes between urban centres. For instance, Exeter scored the highest with a mean NDVI of 0.15, a tree coverage of 11.67%, and an OS Greenspace coverage of 0.05%, and Glasgow the lowest with a mean NDVI of 0.02, a tree cover of 1.95% and an OS Greenspace coverage of 0.00%. We also demonstrated that population size negatively associated with greenness and tree coverage, but not greenspaces, and that green attributes negatively associated with deprivation. This is important because it suggests that health-promoting and biodiversity-supporting resources diminish as population and deprivation increase. Disparities in green infrastructure across the country, along with the population and deprivation-associated trends, are important in terms of socioecological and equity justice. This study provides a baseline and stimulus to help local authorities and urban planners create and monitor equitable greening interventions in urban/city centres. [ABSTRACT FROM AUTHOR]

Glycosylation of CD45RB (RB+) has recently been identified to mark antigen-experienced B cells, independent of their CD27 expression. By using a novel combination of markers including CD45RB glycosylation, CD27 and IgM/IgD isotype expression we segregated human peripheral blood B cell subsets and investigated their IGHV repertoire and in vitro functionality. We observed distinct maturation stages for CD27-RB+ cells, defined by differential expression of non-switched Ig isotypes. CD27-RB+ cells, which only express IgM, were more matured in terms of Ig gene mutation levels and function as compared to CD27-RB+ cells that express both IgM and IgD or cells that were CD27-RB-. Moreover, CD27-RB+IgM+ cells already showed remarkable rigidity in IgM isotype commitment, different from CD27-RB+IgMD+ and CD27-RB- cells that still demonstrated great plasticity in B cell fate decision. Thus, glycosylation of CD45RB is indicative for antigen-primed B cells, which are, dependent on the Ig isotype, functionally distinct. [ABSTRACT FROM AUTHOR]

The rapid increases in ecological footprint and air pollution have followed the fast expansion of the global economy. Urbanization has aggravated environmental strain because of population surge, but the development in the degree of technological innovation would counter balance this negative effect. Hence, in this paper we examine the dynamic impact of urbanization, economic structure, technological innovation and population density on ecological footprint and air quality (PM2.5) in Newly Industrialized Countries (NICs) from 1990 to 2017. The study uses other variables like population density, energy consumption, and life expectancy to find out the long-run relationship among variables. We apply Westerlund co-integration, Mean Group (MG) and Pooled Mean Group (PMG) technique to ascertain the long-run and short-run associations among the variables. For robustness check, we use Augmented Mean Group (AMG) and Common Correlated Mean Group (CCEMG) approach. This study would be the first study in case 10 NICs considered the determinants of ecological footprint and PM2.5. The results reveal that economic growth increases ecological footprint in NICs in long run. Similarly, coefficient of industrialization is positive and significantly related to ecological footprint. However, the service sector shows a negative relation with ecological footprint in NICs. It means service sector helps to improve the environmental quality in long run. Population density, urbanization, energy consumption and life expectancy indicate a positive effect on ecological footprint. Further, in case of PM2.5, the results suggest that economic growth and industrial sectors have high magnitude effects on the PM2.5 than the other variables. The service sector reduces PM2.5, whereas the coefficient value is not significant, but agriculture sector positively influences PM2.5 in NICs. Similarly, population density and urbanization contribution to PM2.5 are positive and significant. Hence, these NICs countries should focus more on the investment in the renewable energy sector and make stringent environmental policy for protecting the nations from environmental issues. [ABSTRACT FROM AUTHOR]

Palynofacies is based on the different types of the dispersed/sedimentary organic matter (DOM/SOM) and has been used as a proficient proxy for the palaeoclimatic reconstructions in sedimentary deposits of various time spans. It has also been acknowledged as an effective tool in the different domains like sequence biostratigraphy, palyno-biostratigraphy, palaeodepositional history, identification for depositional processes, oxic–anoxic environment, and variations in the water depth. It has been emerged as an analytical tool in palaeoclimatic reconstruction, which could complement geophysical and geochemical datasets. Since long palynofacies analysis has been exclusively applied in the marine sediments, it has recently dragged the attention of many researchers as a significant parameter for palaeoclimatic interpretation in continental deposits. In the last few decades, more consideration was focused on palynofacies that have become an essential proxy in the biostratigraphic and other non-biostratigraphic fields due to its requirement in the petroleum industries. The present study provides a basic idea of dispersed organic matter characterization, methodology, interpretations, and its application with special emphasis on the Gondwana deposits. The study also includes the summary of the worldwide distribution of the Gondwana sediments, especially for palaeodepositional settings through palynofacies along with other parameters. [ABSTRACT FROM AUTHOR]

Immunotherapy with antigen-processing independent T cell epitopes (apitopes) targeting autoreactive CD4+ T cells has translated to the clinic and been shown to modulate progression of both Graves' disease and multiple sclerosis. The model apitope (Ac1-9[4Y]) renders antigen-specific T cells anergic while repeated administration induces both Tr1 and Foxp3+ regulatory cells. Here we address why CD4+ T cell epitopes should be designed as apitopes to induce tolerance and define the antigen presenting cells that they target in vivo. Furthermore, we reveal the impact of treatment with apitopes on CD4+ T cell signaling, the generation of IL-10-secreting regulatory cells and the systemic migration of these cells. Taken together these findings reveal how apitopes induce tolerance and thereby mediate antigen-specific immunotherapy of autoimmune diseases. [ABSTRACT FROM AUTHOR]

Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations., (© 2023. The Author(s).)

Summary: Pollen identification and quantification are crucial but challenging tasks in addressing a variety of evolutionary and ecological questions (pollination, paleobotany), but also for other fields of research (e.g. allergology, honey analysis or forensics). Researchers are exploring alternative methods to automate these tasks but, for several reasons, manual microscopy is still the gold standard.In this study, we present a new method for pollen analysis using multispectral imaging flow cytometry in combination with deep learning. We demonstrate that our method allows fast measurement while delivering high accuracy pollen identification.A dataset of 426 876 images depicting pollen from 35 plant species was used to train a convolutional neural network classifier. We found the best‐performing classifier to yield a species‐averaged accuracy of 96%. Even species that are difficult to differentiate using microscopy could be clearly separated.Our approach also allows a detailed determination of morphological pollen traits, such as size, symmetry or structure. Our phylogenetic analyses suggest phylogenetic conservatism in some of these traits. Given a comprehensive pollen reference database, we provide a powerful tool to be used in any pollen study with a need for rapid and accurate species identification, pollen grain quantification and trait extraction of recent pollen. [ABSTRACT FROM AUTHOR]

B lymphocytes are important in secreting antibodies that protect against invading pathogens such as viruses, bacteria, parasites, and also in mediating pathogenesis of allergic diseases and autoimmunity. B lymphocytes develop in the bone marrow and contain heavy and light chains, which upon ligation form an immunoglobulin M (IgM) B cell receptor (BCR) expressed on the surface of naïve immature B cells. Naïve B cells expressing either IgM or IgD isotypes are thought to play interchangeable functions in antibody responses to T cell-dependent and T cell-independent antigens. IgM short-lived plasma cells (SLPCs) and antigen-specific IgM memory B cells (MBCs-M) are critical in the first few days of infection, as well as long-term memory induced by vaccination, respectively. At mucosal surfaces, IgM is thought to play a critical part in promoting mucosal tolerance and shaping microbiota together with IgA. In this review, we explore how IgM structure and BCR signaling shapes B cell development, self and non-self-antigen-specific antibody responses, responses to infectious (such as viruses, parasites, and fungal) and non-communicable diseases (such as autoimmunity and allergic asthma). We also explore how metabolism could influence other B cell functions such as mucosal tolerance and class switching. Finally, we discuss some of the outstanding critical research questions in both experimental and clinical settings targeting IgM. [ABSTRACT FROM AUTHOR]

Persistent and durable immunological memory forms the basis of any successful vaccination protocol. Generation of pre-existing memory B cell and T cell pools is thus the key for maintaining protective immunity to seasonal, pandemic and avian influenza viruses. Long-lived antibody secreting cells (ASCs) are responsible for maintaining antibody levels in peripheral blood. Generated with CD4+ T help after naïve B cell precursors encounter their cognate antigen, the linked processes of differentiation (including Ig class switching) and proliferation also give rise to memory B cells, which then can change rapidly to ASC status after subsequent influenza encounters. Given that influenza viruses evolve rapidly as a consequence of antibody-driven mutational change (antigenic drift), the current influenza vaccines need to be reformulated frequently and annual vaccination is recommended. Without that process of regular renewal, they provide little protection against "drifted" (particularly H3N2) variants and are mainly ineffective when a novel pandemic (2009 A/H1N1 "swine" flu) strain suddenly emerges. Such limitation of antibody-mediated protection might be circumvented, at least in part, by adding a novel vaccine component that promotes cross-reactive CD8+ T cells specific for conserved viral peptides, presented by widely distributed HLA types. Such "memory" cytotoxic T lymphocytes (CTLs) can rapidly be recalled to CTL effector status. Here, we review how B cells and follicular T cells are elicited following influenza vaccination and how they survive into a long-term memory. We describe how CD8+ CTL memory is established following influenza virus infection, and how a robust CTL recall response can lead to more rapid virus elimination by destroying virus-infected cells, and recovery. Exploiting long-term, cross-reactive CTL against the continuously evolving and unpredictable influenza viruses provides a possible mechanism for preventing a disastrous pandemic comparable to the 1918-1919 H1N1 "Spanish flu," which killed more than 50 million people worldwide. [ABSTRACT FROM AUTHOR]

In recent years, efforts to exploit sunlight, a free and abundant energy source, have sped up dramatically. Oxygenic photosynthetic organisms, such as higher plants, algae, and cyanobacteria, can convert solar energy into chemical energy very efficiently using water as an electron donor. By providing organic building blocks for life in this way, photosynthesis is undoubtedly one of the most important processes on Earth. The aim of light-driven catalysis is to harness solar energy, in the form of reducing power, to drive enzymatic reactions requiring electrons for their catalytic cycle. Light-driven enzymes have been shown to have a large number of biotechnological applications, ranging from the production of high-value secondary metabolites to the development of green chemistry processes. Here, we highlight recent key developments in the field of light-driven catalysis using biological components. We will also discuss strategies to design and optimize light-driven systems in order to develop the next generation of sustainable solutions in biotechnology. [ABSTRACT FROM AUTHOR]

The microalga Botryococcus braunii is widely regarded as a potential renewable and sustainable source for industrial applications because of its capability to produce large amounts of metabolically expensive (exo-) polysaccharides and lipids, notably hydrocarbons. A comprehensive and systematic metabolic characterization of the Botryococcus braunii race A strain CCAP 807/2 was conducted within the present study, including the detailed analysis of growth-associated and physiological parameters. In addition, the intracellular metabolome was profiled for the first time and showed growth- and product-specific fluctuations in response to the different availability of medium resources during the cultivation course. Among the identified metabolites, a constant expression of raffinose was observed for the first time under standard conditions, which has until now only been described for higher plants. Overall, the multilayered analysis during the cultivation of strain CCAP 807/2 allowed the differentiation of four distinct physiological growth phases and revealed differences in the production profiles and content of liquid hydrocarbons and carbohydrates with up to 84% of organic dry weight (oDW). In the process, an enhanced production of carbohydrates with up to 63% of oDW (1.36±0.03 g L-1) could be observed during the late linear growth phase, whereas the highest accumulation of extracellular hydrocarbons with up to 24% of oDW (0.66±0.12 g L-1) occurred mainly during the stationary growth phase. Altogether, the knowledge obtained is potentially useful for the general understanding of the overall physiology of Botryococcus braunii and provide important insights into the growth behavior and product formation of this microalga, and is thus relevant for large scale biofuel production and industrial applications. [ABSTRACT FROM AUTHOR]