Memory-like responses in innate immune cells confer nonspecific protection against secondary exposures. A number of microbial agents have been found to induce enhanced or diminished recall responses in innate cells, however, studies investigating the ability of probiotic bacteria to trigger such effects are lacking. Here, we show that priming of human monocytes with a secretome from the gut probiotic bacterium Limosilactobacillus (L.) reuteri induces a mixed secondary response phenotype in monocyte-derived dendritic cells (mo-DCs), with a strong IL-6 and IL-1β response but low TNFα, IL-23 and IL-27 secretion. Instead, blood DC priming with L. reuteri-secretome resembles a tolerant state upon secondary exposure. A similar pattern was found in conventional and gut-like (retinoic acid exposed) DCs, although retinoic acid hampered TNFα and IL-6 production and enrichment of histone modifications in L. reuteri-secretome primed mo-DC cultures. Further, we show that the memory-like phenotype of mo-DCs, induced by priming stimuli, is important for subsequent T helper (Th) cell differentiation pathways and might determine the inflammatory nature of Th cells. We also show enhanced recall responses characterized by robust inflammatory cytokines and lactate production in the gut-like mo-DCs derived from β-glucan primed monocytes. Such responses were accompanied with enriched histone modifications at the promoter of genes associated with a trained phenotype in myeloid cells. Altogether, we demonstrate that a gut commensal-derived secretome prompts recall responses in human DCs which differ from that induced by classical training agents such as β-glucan. Our results could be beneficial for future therapeutic interventions where T cell responses are needed to be modulated.
The Veiki moraine in northern Sweden, a geomorphologically distinct landscape of ice-walled lake plains, has been interpreted to represent the former margin of an intermediate-sized pre–Last Glacial Maximum (LGM) Fennoscandian ice sheet, but its age is debated as either marine isotope stage (MIS) 5c or MIS 3. We have applied optically stimulated luminescence (OSL) and radiocarbon dating to four sites within the northern part of the Veiki moraine to establish its chronology. The radiocarbon ages provide only minimum ages and most OSL ages have low precision due to poor luminescence characteristics and problems with incomplete bleaching, leading to two alternative ages. In either case, the OSL dating places the Veiki moraine formation in MIS 3 (best estimate 56–39 ka). Sedimentation continued in the low-lying centers of some plateaus (ice-walled lake plains) during MIS 3 and during the Holocene, with a break during the Last Glacial Maximum when the area was ice covered. We speculatively constrain the broad timing further by relating the sequence of events to other climate records. We suggest that ice margin retreat to the west of the Veiki area took place during Greenland Interstadial (GI) 16.1 (58.0–56.5 ka) and that limited ice advances, which led to debris-covered ice margins in the Veiki zone, occurred during the following stadials GS-16.1 to 15.1 (56.5–54.2 ka). The GI-14 interstadial, which began 54.2 ka and lasted ~5.9 ka, could then be the period when the ice within the dead-ice landscape melted, first leading to ice-walled lakes and later to the inversed topography characteristic of the Veiki landscape. ************************************ Full text available open access at https://doi.org/10.1080/15230430.2022.2091308
Social-ecological systems (SES) research has emerged as an important area of sustainability science, informing and supporting pressing issues of transformation towards more sustainable, just and equitable futures. To date, much SES research has been done in or from the Global North, where the challenges and contexts for supporting sustainability transformations are substantially different from the Global South. This paper synthesises emerging insights on SES dynamics that can inform actions and advance research to support sustainability transformations specifically in the southern African context. The paper draws on work linked to members of the Southern African Program on Ecosystem Change and Society (SAPECS), a leading SES research network in the region, synthesizing key insights with respect to the five core themes of SAPECS: (i) transdisciplinary and engaged research, (ii) ecosystem services and human well-being, (iii) governance institutions and management practices, (iv) spatial relationships and cross-scale connections, and (v) regime shifts, traps and transformations. For each theme, we focus on insights that are particularly novel, interesting or important in the southern African context, and reflect on key research gaps and emerging frontiers for SES research in the region going forward. Such place-based insights are important for understanding the variation in SES dynamics around the world, and are crucial for informing a context-sensitive global agenda to foster sustainability transformations at local to global scales.
The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.
Background Barley has been bred for more than a century in the Nordic countries, with dramatic improvements of yield traits. In this study we investigate if this has come at the cost of lower grain protein and micronutrient (iron, zinc) content, by analysing 80 accessions representing four different improvement stages. We further re-sequenced the two grain protein content associated genes HvNAM-1 and HvNAM-2 in full and performed expression analyses of the same genes to search for genetic associations with nutrient content. Results We found higher thousand grain weight in barley landraces and in accessions from the late improvement group compared to accessions from the mid of the twentieth century. Straw length was much reduced in late stage accessions. No significant temporal decrease in grain protein, iron or zinc content during twentieth century Nordic crop improvement could be detected. Out of the 80 accessions only two deviant HvNAM-1 sequences were found, represented by one accession each. These do not appear to be correlated to grain protein content. The sequence of HvNAM-2 was invariable in all accessions and no correlations between expression levels of HvNAM-1 and HvNAM-2 and with grain protein content was found. Conclusions In contrast to studies in wheat, where a strong negative correlation between straw length and grain protein and micronutrient content has been found, we do not see this relationship in Nordic barley. The last 60 years of breeding has reduced straw length but, contrary to expectations, not protein and micronutrient content. Variation in grain protein and micronutrient content was found among the Nordic barley accessions, but it is not explained by variation of HvNAM genes. This means that HvNAM is an unexploited source of genetic variation for nutrient content in Nordic barley.
Male colour patterns of the Trinidadian guppy ( Poecilia reticulata ) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.
Background Merlin’s grass ( Isoetes , Isoetaceae, Lycopsida), is the extant remnant of the isoetalean wood-producing lycopsids that originated during the Paleozoic, possibly in aquatic or boggy habitats. Modern day species are aquatic, semi-aquatic or terrestrial and occur almost worldwide. They display little morphological variation; the lobed corm has helically arranged leaves with internal air channels and basal sporangia. Genetic variation has also proven limited, which has hampered phylogenetic inference. We investigate evolutionary relationships in Isoetes , using molecular data and an extended sample of species compared to previous work, adding species that have never before been included in a phylogenetic study. Results Our results reveal an unexpected discovery of an “ Amborella syndrome” in Isoetaceae: a single poorly known species is sister to the remaining family. The species, Isoetes wormaldii , is a rare endemic to the Eastern Cape of South Africa. Its leaves are flattened with a rounded point, which sharply contrasts with the awl-shaped leaves of most other species of Isoetes . The remaining species of Isoetes are resolved in five major clades, also indicated in previous work. While the phylogeny shows geographic structure, the patterns are complex. For example, tropical-southern African species occur in at least five clades, and Indian, Australian and Mediterranean species in at least three clades each. Conclusion The evolutionary and biogeographical history of Isoetes is not easily explained, and may conceivably include ample extinction and a mixture of ancient and more recent processes. Previously shown difficulties with node age estimation increase the problem. The here demonstrated sister-relationship between the phylogenetically, morphologically and genetically distinct Isoetes wormaldii and the remaining family appears to bridge the morphological gap between Isoetes and its extinct relatives, although further studies are needed. Moreover, it shortens the branch length to its living sister genus Selaginella , and may enhance node age estimation in future studies. Isoetes wormaldii is critically endangered, known only from one (to a few) minor populations. Immediate actions need to be taken if we want to prevent this unique species from going extinct.
Humans have deliberately scented their environment for purpose or pleasure for millennia. In the contemporary marketplace most consumers prefer and purchase scented versions of common household products. However, the drivers of this consumer preference have not been elucidated. To explain the attraction to scent in household products we propose a novel three-factor framework, comprising functional benefits (malodor mitigation, base odor coverage, freshening), in -use experience benefits (cleanliness, efficacy, pleasure), and emotional benefits (increasing in confidence, mood and nostalgia). To support this framework, we present new data from a market research survey on US consumer purchasing habits and attitudes towards home cleaning, laundry, and air freshening products. Further substantiating our framework, a focused review of olfactory psychological science illustrating the central role of scent in cognition, wellbeing, motivated behavior, and social behavior, as well as sensory marketing research highlights the benefits and implications of scent in consumer household products. Based on our three-factor framework we go on to discuss the potential for scent to influence health and raise issues to consider (such as potential negative responding to fragranced products). We conclude by showcasing new opportunities for future research in olfactory science and on scented household products that can advance the positive impacts of scent.
Objective The present study investigates if symptoms of COVID-19 contagion in different social contexts (cohabitants, family, acquaintances, and others) are associated with university students' own self-reported symptoms of COVID-19 contagion, mental health, and study capacity. This was investigated by a cross-sectional survey administrated in Sweden during the first wave of the COVID-19 pandemic, at the time when universities were locked down to limit viral spread and contagion. Results Mild to moderate symptoms of COVID-19 in cohabitants and family members were associated with student’s self-reported symptoms of contagion, while no associations could be seen in relation to mental health and study capacity. Symptoms of COVID-19 contagion in acquaintances and others were not associated with students’ self-reported symptoms, nor with their mental health and study capacity. To conclude, during the initial lockdown of universities students’ self-reported symptoms of contagion were mainly associated with cohabitants and family members, while symptoms of contagion in different social contexts were not associated with mental health and study capacity. Findings suggest that lockdown of universities may have contributed to limiting infection pathways, while still allowing students to focus on their studies despite significant contagion among others known to the student.
In rod-shaped bacteria, morphological plasticity occurs in response to stress, which blocks cell division to promote filamentation. We demonstrate here that overexpression of the patatin-like phospholipase variant CapV Q329R , but not CapV, causes pronounced sulA -independent pyridoxine-inhibited cell filamentation in the Escherichia coli K-12-derivative MG1655 associated with restriction of flagella production and swimming motility. Conserved amino acids in canonical patatin-like phospholipase A motifs, but not the nucleophilic serine, are required to mediate CapV Q329R phenotypes. Furthermore, CapV Q329R production substantially alters the lipidome and colony morphotype including rdar biofilm formation with modulation of the production of the biofilm activator CsgD, and affects additional bacterial traits such as the efficiency of phage infection and antimicrobial susceptibility. Moreover, genetically diverse commensal and pathogenic E. coli strains and Salmonella typhimurium responded with cell filamentation and modulation in colony morphotype formation to CapV Q329R expression. In conclusion, this work identifies the CapV variant CapV Q329R as a pleiotropic regulator, emphasizes a scaffold function for patatin-like phospholipases, and highlights the impact of the substitution of a single conserved amino acid for protein functionality and alteration of host physiology.
The interest in operating autonomous vehicles is growing and several demonstration sites using automated shuttles have been established all over the world. Major work is involved in setting up an automated shuttle operation that involves more than identifying the relevant site, including adhering to current regulations and obtaining approval, as well as a considerable amount of preparation and commissioning required at the site. The shuttle must pass relevant national vehicle regulations, and the operation site has to undergo a site assessment. This paper is based on lessons learned achieved from setting up automated shuttle operations in three different areas in Europe: Brussel (Belgium), Linköping (Sweden) and Turin (Italy). The focus is on the practical aspects of operation. Through the experience we have gained of setting up demonstration sites at three locations in Europe, we have identified the need to summarise the lessons learned from preparing AV shuttle operation sites in order to facilitate the implementation of other operation sites. Hence, this paper aims to consolidate lessons learned during preparation and implementation of automated shuttle operations in near urban environments and to identify the path toward future implementation The three sites operate different brands and number of shuttles, different types of infrastructure and varying local conditions. The focus here was on generic lessons learned and not to understand differences between brands and operators. It is clear that further development of the AV shuttles is vital to ensure that they operate smoothly in complex traffic situations considering lane and road width, shared spaces, snow, dust, rain, leaves, birds, etc. Adapting the road infrastructure to enable the shuttles to run in the autonomous mode should be avoided, instead the shuttle development should prioritise fitting into the existing traffic environment and eco system. Mitigation areas have been identified covering: road infrastructure, weather dependant operation, season dependent operation, improvement of localisation, digital infrastructure, design and working conditions, and citizens’ user experience.
Background Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. Results The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with “population analysis” to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1–11, 2015). Conclusions This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.
Here we describe the structure, the high-pressure, low-temperature (HP-LT) metamorphism and tectonic evolution of the Briançonnais distal margin units from the south Western Alps. The studied area extends southwest of the Dora-Maira (U)HP basement units and east-southeast of the classical Briançonnais nappes. A new structural map accompanied by geological profiles shows the thrusting of the oceanic nappes (Monviso and Queyras units) onto the distal Briançonnais units (D1 and D2 late Eocene deformation phases) under blueschist-facies conditions. Subsequent deformation during the Early Oligocene (D3 deformation phase) took place under greenschist-facies conditions and was associated with back-folding and -thrusting in the units overlying the Dora-Maira massif and with exhumation related to normal reactivation of former thrusts within the latter massif. Two large cover units, detached from their former distal Briançonnais basement, are redefined as the Maira-Sampeyre and Val Grana Allochthons (shortly: Maira-Grana Allochthons = MGA) including, (i) the Val Maira-Sampeyre unit involving Lower and Middle Triassic formations, seemingly detached from the Dora-Maira units during the subduction process, and (ii) the Val Grana unit with Middle-Upper Triassic and Early-Middle Jurassic formations, which was probably detached from the Maira-Sampeyre unit and correlates with the “Prepiemonte units” known from the Ligurian Alps to the Swiss Prealps. Three major shear zones involving tectonic mélanges of oceanic and continental rocks at the base of the Val Grana, Maira-Sampeyre and Dronero units testify to an early phase of exhumation within the subduction channel in front of the Adria plate. We present a new metamorphic map based on published and new petrological data, including new thermometric data obtained by Raman spectroscopy of carbonaceous material (RSCM). The T RSCM values range from ~ 400 °C to > 500 °C, going from the most external Val Grana unit and overlying Queyras schists to the uppermost Dora-Maira unit. During the Late Triassic, the width of the Briançonnais s.l. domain can be restored at ~ 100 km, whereas it reached ~ 150 km after the Jurassic rifting. A significant, second rifting event affected the Briançonnais domain during the Late Cretaceous-Paleocene, forming the Longet-Alpet chaotic breccias, which deserve further investigations.
The Laser Interferometer Space Antenna (LISA) has the potential to reveal wonders about the fundamental theory of nature at play in the extreme gravity regime, where the gravitational interaction is both strong and dynamical. In this white paper, the Fundamental Physics Working Group of the LISA Consortium summarizes the current topics in fundamental physics where LISA observations of gravitational waves can be expected to provide key input. We provide the briefest of reviews to then delineate avenues for future research directions and to discuss connections between this working group, other working groups and the consortium work package teams. These connections must be developed for LISA to live up to its science potential in these areas.
Carbon border levies have been suggested as an important tool for ramping up climate action. Such a levy is being negotiated as part of the EU’s Green Deal, with input from public consultations. The success of the EU’s carbon border adjustment mechanism (CBAM) will depend on its design and acceptance. While most analyses focus on resistance from the EU’s major external trade partners, this article analyses the views of non-state actors within the EU. Their views will be decisive for the cohesion and determination of the EU as the CBAM proposal encounters external resistance. Examining the views of European business and civil society organizations expressed by 276 respondents in the EU’s public consultation, we show that there is general support for CBAM but divergent views on its purpose and on what to do about the allocation of free allowances in the EU Emissions Trading System, sectoral coverage, exemptions for third countries, export rebates and emissions scope. The success and strength of CBAM will depend on whether the EU is able to resolve these design issues and reach compromises between the opposing views of business and civil society. Graphical Abstract
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