32151 research outputs found
Sort by
Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth’s history
Full text linkThe transition from anaerobic to aerobic life was a pivotal adaptation in Earth’s history, yet the timing and genomic drivers remain poorly resolved. Traditional approaches relying on oxygen-utilizing genes need improvement for obligate anaerobes and fragmentary environmental genomes, where gene absence may reflect poor assembly rather than phenotype. We developed a machine learning model (GBDT40-LR) to predict microbial oxygen requirements using 40 broadly conserved genes, 35 without direct oxygen roles. This approach overcomes incompleteness biases in environmental genomes. Applied to 80,787 bacterial genomes [including metagenome-derived assemblies (MAGs)], the model classified 42,014 aerobes and 38,775 anaerobes, enabling large-scale ancestral reconstruction. Molecular clock dating indicates an emergence of aerobic bacterium prior to the Great Oxidation Event (GOE, 2.5 to 2.3 Ga), likely around ~2.7 Ga. Aerobic lineages subsequently diversified during the GOE and Neoproterozoic Oxygenation Event (NOE, 0.8 to 0.55 Ga), with persistent anaerobe diversity across Earth’s oxygenation. This establishes that aerobic bacteria originated planetary oxygenation, potentially by 200 to 400 My, providing insights into phenotypic evolution and prolonged anaerobe–aerobe coexistence.Peer reviewe
Precise constraints on the energy budget of WASP-121 b from its JWST NIRISS/SOSS phase curve
Full text linkFunding: This project was undertaken with the financial support of the Canadian Space Agency through a NEAT/GTO grant. The contributions from RF were supported in part by grant #2019-1403 from the Heising-Simons Foundation. N.B.C. acknowledges support from an NSERC Discovery Grant, a Tier 2 Canada Research Chair, and an Arthur B. McDonald Fellowship and thanks the Trottier Space Institute and l’Institut de recherche sur les exoplanétes for their financial support and dynamic intellectual environment. L.D. is a Banting and Trottier Postdoctoral Fellow and acknowledges support from the Natural Sciences and Engineering Research Council (NSERC) and the Trottier Family Foundation. S.P. acknowledges support from the Swiss National Science Foundation under grant 51NF40_205606 within the framework of the National Centre of Competence in Research PlanetS. R.J.M. is supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51513.001, awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS 5-26555. D.L. acknowledges financial support from NSERC and FRQNT. C.P.-G. acknowledges support from the E. Margaret Burbidge Prize Postdoctoral Fellowship from the Brinson Foundation. J.D.T. acknowledges funding support by the TESS Guest Investigator Program G06165.Ultra-hot Jupiters exhibit day-to-night temperature contrasts upwards of 1000 K due to competing effects of strong winds, short radiative timescales, magnetic drag, and H2 dissociation/recombination. Spectroscopic phase curves provide critical insights into these processes by mapping temperature distributions and constraining the planet’s energy budget across different pressure levels. Here, we present the first NIRISS/SOSS phase curve of an ultra-hot Jupiter, WASP-121 b. The instrument’s bandpass [0.6–2.85 μm] captures an estimated 50%–83% of the planet’s bolometric flux, depending on orbital phase, allowing for unprecedented constraints on the planet’s global energy budget; previous measurements with HST/WFC3 and JWST/NIRSpec/G395H captured roughly 20% of the planetary flux. Accounting for the unobserved regions of the spectrum, we estimate effective day- and nightside temperatures of Tday = 2717 ± 17 K and Tnight = 1562+18-19 K corresponding to a Bond albedo of AB = 0.277 ± 0.016 and a heat recirculation efficiency of ε = 0.246 ± 0.014. Matching the phase-dependent effective temperature with energy balance models yields a similar Bond albedo of 0.3 and a mixed layer pressure of 1 bar consistent with photospheric pressures, but unexpectedly slow winds of 0.2 km s−1, indicative of inefficient heat redistribution. The shorter optical wavelengths of the NIRISS/SOSS Order 2 yield a geometric albedo of Ag = 0.093+0.029-0.027 (3σ upper limit of 0.175), reinforcing the unexplained trend of hot Jupiters exhibiting larger Bond than geometric albedos. We also detect near-zero phase curve offsets for wavelengths above 1.5 μm, consistent with inefficient heat transport, while shorter wavelengths potentially sensitive to reflected light show eastward offsets.Peer reviewe
Critical exponents and dimension for generalised limit sets
No full textFunding: JMF was financially supported by a Leverhulme Trust Research Project Grant (RPG-2019- 034) and an EPSRC Standard Grant (EP/Y029550/1).There is a beautiful and well-studied relationship between the Poincaré exponent and the fractal dimensions of the limit set of a Kleinian group. Motivated by this, given an arbitrary discrete subset of the unit ball we define a critical exponent and investigate how it relates to the fractal dimensions of the associated generalised limit set.Peer reviewe
Easy to access iridium(III) NHC complexes as highly photoreducing photocatalysts having high photostability
No full textFunding: The authors thank Johnson Matthey for financial support in the form of an i-CASE award (PhD studentship to M.G.). The authors thank EPSRC for financial support (grants EP/W522259/1, EP/W007517/1, EP/Z535291/1, and EP/M02105X/1). The authors would like to thank the European Union H2020 Research and Innovation Program for funding under the Marie Skłodowska-Curie grant agreement (PhotoReAct, no. 956324).Here, we investigate the potential of and reactivity differences of the meridional and facial isomers of an Ir(III) NHC photocatalyst Ir(pmi)3 . Compared with the archetypal photocatalyst fac-Ir(ppy)3 , both mer- and fac-Ir(pmi)3 possess significantly higher triplet energies (ET = 3.28 and 3.30 eV, respectively) and are more photoreducing (E*ox = −2.72 and −2.67 V vs. saturated calomel electrode [SCE], respectively). Across a range of photoinduced energy transfer, photoredox, and metallaphotoredox catalysis reactions, these two photocatalysts could activate substrates having Ered as high as −2.60 V vs. SCE and ET as high as 3.00 eV. Across the set of reactions, both complexes consistently achieve higher yields than both fac -Ir(ppy)3 and [Ir(dF(CF3)ppy)2(dtbbpy)]PF6 . As a result of the more robust NHC ligands, under the reaction conditions, Ir(pmi)3 exhibited significantly improved photostability compared to fac-Ir(ppy)3 . This work highlights Ir(pmi)3 as an easy-to-synthesize, powerful, and versatile photocatalyst that should be a welcome addition to the toolbox of photocatalysts for the synthetic organic chemist.Peer reviewe
Choosy dispersal promotes the evolution of altruism
No full textFunding: H2020 ERC 'Sociocomplexity - new paradigms for understanding complex group-level adaptation' (grant agreement ID 771387).Altruistic behaviour is evolutionarily favoured through the action of kin selection. A simple mechanism for kin selection is population viscosity, whereby individuals do not move very far over the course of their lives, such that even indiscriminate helping of neighbours is liable to benefit one's genetic relatives. However, population viscosity is also associated with intensified resource competition among kin, which acts to inhibit the evolution of altruism. In standard models of population structure, these opposing effects of viscosity exactly cancel so that the evolutionary potential for altruism is completely invariant with respect to the rate of dispersal. Here, we investigate the consequences of load-balancing dispersal—whereby dispersers exhibit a preference for settling in less-crowded areas—for the evolution of altruism. Using mathematical modelling and individual-based computer simulations, we find that load-balancing dispersal dramatically reduces the kin-competition consequences of altruism, and thereby strongly promotes the evolution of altruism in viscous populations. We discuss other implications of such load-balancing dispersal for social evolution.Peer reviewe
Immigrant and refugee mobility across the urban–rural continuum in three European countries
No full textFunding: This paper is part of the MigrantLife project that has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No. 834103). The paper also received funding from the Swiss National Science Foundation for the project Magnet Cities? Immigrants’ Inclusion Across the Urban–Rural Continuum (Grant: 10.004.608).International migration has historically been an urban phenomenon. Despite the increasing presence of immigrants in non-urban areas and political initiatives aimed at regionalization, research in Europe continues to exhibit a pronounced urban analytical bias. This paper examines the geographies of immigrant and refugee settlement along the urban–rural continuum in Sweden, Germany, and Switzerland. Using (multistate) event history models, we first examine changes in migration stocks in urban, suburban, and rural municipalities, emphasizing the role of immigrant subgroups in regional population changes. Second, we analyze internal origin–destination flux to enhance our understanding of the spatial adjustment processes of immigrants in the context of new immigrant destinations in Europe. Results suggest that immigrants contribute little to suburbanization and ruralization processes, with both initial settlement and secondary moves predominantly directed toward urban areas. EU and non-EU immigrants exhibit stable trajectories post-arrival; in contrast, refugees subjected to a dispersal policy tend to relocate in significant proportions to urban areas once mobility restrictions are lifted. In the three countries, secondary moves by refugees have resulted in an increased concentration of this population in urban areas, reaching proportions comparable to those of the non-European immigrant group not subjected to this policy. The consistency of this finding across the three countries raises significant questions regarding the effectiveness of the dispersal policy from a demographic perspective. Furthermore, transitions from urban to suburban or rural municipalities remain uncommon and do not demonstrate clear associations with the duration of residence or socioeconomic status, as predicted by the spatial assimilation model.Peer reviewe
Long-read spatial transcriptomics of patient-derived clear cell renal cell carcinoma organoids identifies heterogeneity and transcriptional remodelling following NUC-7738 treatment
No full textFunding: The authors acknowledge Research Computing at the James Hutton Institute for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grants BB/S019669/1 and BB/X019683/1), use of which has contributed to the results reported within this paper.Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer and is marked by pronounced intra-tumoural heterogeneity that complicates therapeutic response. Patient-derived organoids offer a physiologically relevant model to capture this diversity and evaluate treatment effects. When integrated with spatial transcriptomics, they might enable the mapping of spatially resolved transcriptional and isoform-level changes within the tumour microenvironment. Methods: We established a robust workflow for generating patient-derived ccRCC organoids, that are not passaged and retain original cellular components. These retain key features of the original tumours, including cancer cell, stromal, and immune components. Results: Spatial transcriptomic profiling revealed multiple transcriptionally distinct regions within and across organoids, reflecting the intrinsic heterogeneity of ccRCC. Isoform-level analysis identified spatially variable expression of glutaminase (GLS) isoforms, with heterogeneous distributions of both the GAC and KGA variants. Treatment with NUC-7738, a phosphoramidate derivative of 3′-deoxyadenosine, induced marked transcriptional remodelling of organoids, including alterations in ribosomal and mitochondrial gene expression. Conclusions: This study demonstrates that combining long-read spatial transcriptomics with patient-derived organoid models provides a powerful and scalable approach for dissecting gene and isoform-level heterogeneity in ccRCC and for elucidating spatially resolved transcriptional responses to novel therapeutics.Peer reviewe
Contextualising multimorbidity in people who use drugs : analysis of drug-death decedents in Scotland
No full textFunding: Data acquisition was funded by a grant from the Chief Scientist Office of the Scottish Government HIPS/19/32.Objectives: To characterise hospital-treated multimorbidity patterns in people who subsequently died a drug-related death in Scotland, and to identify clinically meaningful associations among conditions and decedent to inform prevention and care. Methods: A register-based retrospective cohort study using nationally linked hospital admission (1996–2019) and mortality (2008–2019) records for 5,749 decedents. We identified hospital admissions for Elixhauser comorbidities using ICD-10 codes. Correlation analysis, network analysis, and Bayesian clustering were used to describe co-occurring conditions and identify patient clusters with distinct comorbidity profiles. Results: Over half (50.9%) of decedents had at least one admission for an Elixhauser comorbidity. The most frequent were related to alcohol use (38.2%), drug use (29.1%), other neurological disorders (18.0%, mainly epilepsy/seizures/anoxic brain injury), depression (15.2%), and psychoses (12.5%). Network analysis highlighted drug use, alcohol use, psychoses, depression, and neurological disorders as central conditions. Bayesian clustering identified seven distinct patient clusters, including groups characterised by: high psychiatric and drug-use admissions; extensive physical comorbidities; alcohol and liver disease; dominant neurological issues and depression. Conclusions: Individuals experiencing drug-related deaths exhibit substantial multimorbidity with distinct patterns often dominated by substance use and mental ill-health but also including significant physical health clusters. These distinct profiles underscore the need for integrated, tailored care strategies addressing substance use, psychiatric, and physical health needs to mitigate mortality risk.Peer reviewe
Function from confinement : ligand-coated nanoparticles as functional materials
Full text linkFunding: E.R.K. and P.P. are very grateful to the Royal Society for the support (Grant ID: IES\R3\203190). V.S. is profoundly thankful for the financial support provided by the National Science Centre of Poland (Grant OPUS 25 no. 2023/49/B/ST5/01472). F.M. is grateful to AIRC (Italian Association for Cancer Research) for support (AIRC IG Grant 25003). G.R. thankfully acknowledges the Interdisciplinary Thematic Institute ITI-CSC via the IdEx Unistra (ANR-10-IDEX-0002) within the program Investissement d’Avenir. B.A.G. is grateful for the generous support from the Institute for Basic Science, Korea (award IBS-R020-D1). Some early work described in this paper was also supported by the National Science Center, Poland (grant Maestro, # 2018/30/A/ST5/00529).For nanoparticles stabilized by self-assembled monolayers, the surface-bound molecular species not only modify the core material properties but also provide a handle for interaction with other components, whether they are molecular, nanoscale, or even macroscopic. Importantly, when confined to nanosurfaces, these organic entities exhibit emergent properties that impart unique functionalities to the underlying nanomaterial. In this Review, we examine how these capabilities originate from the structural organization and collective interactions within on-nanoparticle self-assembled monolayers, drawing on examples of quasi-spherical nanoparticles smaller than ca. 8 nm in size. Our focus spans four key categories of function: (i) catalysis and chemical transformation under nanoconfinement, (ii) molecular recognition and sensing, (iii) switching and adaptation, and (iv) programmable nanoparticle assembly. By adopting a systems-chemistry perspective to identify how function is defined by chemical constitution, we elucidate design principles and strategies that we envisage can be broadly applied to a variety of hybrid organic–inorganic nanosystems. We also highlight the current challenges and future opportunities in the field of functional nanoparticles stabilized by self-assembled monolayers. Our aim is to motivate the community to shift toward a perspective in which the organic layer is understood as an active driver of the system functionality rather than a passive component. By harnessing its dynamic and adaptative nature, researchers can design functionally sophisticated and chemically programmable nanomaterials, unlocking unexplored possibilities in active materials, nanocatalysis, molecular recognition, sensing, and delivery.Peer reviewe
Access Repository Dashboard
Do you manage St Andrews Research Repository? Access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard!