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Non-specific electrostatic interactions and the conversion of horseshoe crab haemocyanin into a phenoloxidase
Get PDFFunding: Some of the initial experimental work was financed by the University of Stirling and supplemented by Swansea University.Haemocyanin is a haemolymph (blood)-based protein and the functional equivalent to haemoglobin – supplying tissues with oxygen in decapod crustaceans, chelicerates, and shelled molluscs. In addition to oxygen transport, haemocyanin plays several roles in innate immunity, wound healing, and ecdysis. Under certain conditions in vitro and in vivo, horseshoe crab (Limulus polyphemus) haemocyanin is converted into a phenoloxidase-like enzyme, yet the protein-ligand interactions associated with this conversion remain unclear. Negatively charged ligands, such as phosphatidylserine and sodium dodecyl sulphate, represent effective endogenous and exogenous activators, respectively. Herein, we explored the nature of the interaction between haemocyanin and phosphatidylserine. We used several spectroscopic techniques and phenoloxidase assays to follow the electrostatic interactions. Manipulating the ionic strength of the assay resulted in less enzyme activity, and reversed haemocyanin conformational changes associated with phosphatidylserine binding (confirmed by fluorescence emission spectra). The addition of wild type and rearranged peptides – mimicking the P181 to K196 region close to the active site of haemocyanin subunit II – to phenoloxidase assays resulted in less product (dopachrome) formation. We propose that non-specific electrostatic interactions between haemocyanin and endogenous activators such as phosphatidylserine facilitate the switch to a phenoloxidase-like enzyme.Peer reviewe
On the nature of improper hydrogen bonding in RCH2F and RCHF2 motifs
Get PDFFunding: D.O'H., R.A.C. and B.A.P. thank FAPESP for a Young Researcher Award (#2018/03910-1) and a scholarship (#2022/10156-7 and #2023/14064-2), respectively. FAEPEX is acknowledged by a Fellowship (#3472/23). D.O'H acknowledges support from EPSRC (EP/X038904/1).The RCH2F and RCHF2 groups are substituents of interest in medicinal and agrochemicals products. They have a polar aspect relative to the methyl (RCH3) or trifluoromethyl (RCF3) groups which results in a lowering of Log P's (water affinity). Here we use a computational approach to explore the nature of the interaction between RCH2F and RCHF2 in methanes and ethanes with chloride ion (and water), as a hydrogen bonding acceptor. A key observation is that the hydrogen atoms geminal to the fluorine(s) become less positively charged with increasing fluorination, a trend anticipated to weaken, not strengthen, their hydrogen bonding interactions. However this study demonstrates a dominating role for the electrostatic interaction of the acceptor with the CF carbons and profiles a shift in negative charge density from hydrogen to the carbon and fluorine(s) as chloride ion (or water) approach. The common occurrence of blue shifts (shortening C─H length) in these ‘improper’ or ‘non-classical’ hydrogen bonds is also explored and is correlated with the electrostatic interactions between the acceptor and the carbon atoms. These observations are extended to C3─C6 alicyclic rings containing these motifs and predict particularly strong interactions energies between chloride ion and specifically designed organo-fluoro alicycles.Peer reviewe
JWST-TST DREAMS : quartz clouds in the atmosphere of WASP-17b
Get PDFFunding: D.G. acknowledges funding from the UKRI STFC Consolidated grant No. ST/V000454/1. H.R.W. was funded by UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee (grant No. EP/Y006313/1). A.G. acknowledges support from the Robert R. Shrock Graduate Fellowship. J.G. acknowledges funding from SERB research grant No. SRG/2022/000727. R.J.M. is supported by NASA through the NASA Hubble Fellowship grant No. 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. We acknowledge the MIT SuperCloud and Lincoln Laboratory Supercomputing Center for providing high performance computing resources that have contributed to the research results reported within this paper. Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at Ames Research Center. N.E.B. acknowledges support from NASA's Interdisciplinary Consortia for Astrobiology Research (grant No. NNH19ZDA001N-ICAR) under award number 19-ICAR19_2-0041.Clouds are prevalent in many of the exoplanet atmospheres that have been observed to date. For transiting exoplanets, we know if clouds are present because they mute spectral features and cause wavelength-dependent scattering. While the exact composition of these clouds is largely unknown, this information is vital to understanding the chemistry and energy budget of planetary atmospheres. In this work, we observe one transit of the hot Jupiter WASP-17b with JWST's MIRI LRS and generate a transmission spectrum from 5-12 μm. These wavelengths allow us to probe absorption due to the vibrational modes of various predicted cloud species. Our transmission spectrum shows additional opacity centered at 8.6 μm, and detailed atmospheric modeling and retrievals identify this feature as SiO2(s) (quartz) clouds. The SiO2(s) clouds model is preferred at 3.5-4.2σ versus a cloud-free model and at 2.6σ versus a generic aerosol prescription. We find the SiO2(s) clouds are comprised of small ~0.01 μm particles, which extend to high altitudes in the atmosphere. The atmosphere also shows a depletion of H2O, a finding consistent with the formation of high-temperature aerosols from oxygen-rich species. This work is part of a series of studies by our JWST Telescope Scientist Team (JWST-TST), in which we will use Guaranteed Time Observations to perform Deep Reconnaissance of Exoplanet Atmospheres through Multi-instrument Spectroscopy (DREAMS).Peer reviewe
Particle algorithms for animal movement modelling in receiver arrays
Get PDFFunding: Department of Systems Analysis, Integrated Assessment and Modelling, Eawag Swiss Federal Institute of Aquatic Science and Technology.1. Particle filters and smoothers are sequential Monte Carlo algorithms used to fit non-linear, non-Gaussian state-space models. These algorithms are well placed to fit process-oriented models to animal-tracking data, especially in receiver arrays, but to date they have received limited attention in the ecological literature. 2. We introduce a Bayesian filtering–smoothing algorithm that reconstructs individual movements and patterns of space use from animal-tracking data, with a focus on passive acoustic telemetry systems. Within a sound probabilistic framework, the methodology integrates the movement process and the observation processes of disparate datasets, while correctly representing uncertainty. In a simulation-based analysis, we compare the performance of our algorithm to the prevailing heuristic methods used to study movements and space use in passive acoustic telemetry systems and analyse algorithm sensitivity. 3. We find the particle smoothing methodology outperforms heuristic methods across the board. Particle-based maps represent simulated movements more accurately, even in dense receiver arrays, and are better suited to analyses of home ranges, residency and habitat preferences. 4. This study sets a new state-of-the-art for movement modelling in receiver arrays. Particle algorithms provide a robust, flexible and intuitive modelling framework with potential applications in many ecological settings.Peer reviewe
Global tracking of marine megafauna space use reveals how to achieve conservation targets
Get PDFFunding: D.W.S. acknowledges funding from ERC-2019-ADG 883583OCEAN DEOXYFISH and NERC NE/R00997X/1. V.M.E. acknowledges funding from MCIN/AEI/10.13039/501100011033 (PID2020-114324GB-C22). B.J.G. acknowledges the Natural Environment Research Council (NERC), Darwin Initiative. .C.H. acknowledges funds provided by NERC and the Department for Business, Energy and Industrial Strategy. M.A.C.N. acknowledges the petrel tracking program and Malcolm Nicollwere supported by NERC (grant NE/H5081500) with in situ support from MWF and NPCS. D.W.S. further acknowledges additionalfield research support provided by the Save Our Seas Foundation (grants 45, 87, 308) and theNERC Oceans 2025 Strategic Research Programme. Wanless wasfunded by the NERC Centre for Ecology & Hydrology. F.C.W. was funded by the UK Natural Environment Research Council (NERC) through a Universityof Southampton INSPIRE DTP Studentship. The project also received funding from theEuropean Union (Marie Curie grant nos. FP6 and FP7).The recent Kunming-Montreal Global Biodiversity Framework (GBF) sets ambitious goals but no clear pathway for how zero loss of important biodiversity areas and halting human-induced extinction of threatened species will be achieved. We assembled a multi-taxa tracking dataset (11 million geopositions from 15,845 tracked individuals across 121 species) to provide a global assessment of space use of highly mobile marine megafauna, showing that 6300Target 3) will be insufficient for marine megafauna’s effective conservation, leaving important areas exposed to major anthropogenic threats. Coupling area protection with mitigation strategies (e.g., fishing regulation, wildlife-traffic separation) will be essential to reach international goals and conserve biodiversity. Many large marine animals are threatened with extinction. To address this problem, the Kunming-Montreal Global Biodiversity Framework has set a goal of protecting, conserving, and managing at least 30s oceans. However, the effectiveness of area-based conservation may be limited for highly mobile marine species, especially when there is limited understanding of the spatial and temporal dynamics of animal movement in the oceans. Sequeira et al. compiled tracking data from thousands of large marine vertebrates representing more than 100 species and identified important migratory corridors and areas where many species reside (see the Perspective by Gerber and Davis). Their findings show hotspots of movement and reveal that 30 particularly considering the distribution of threats to biodiversity. —Bianca LopezPeer reviewe
Friendships to perish and friendships to cherish : corporate political tactic and earnings management method
Get PDFCritical of a literature which examines corporate political connections with scant attention to their dynamic nature, we blend political theory with inter-organizational exchange research to propose and test a framework based on which firms’ earnings management (EM) method can vary predictably with their political tactic. Using hand-collected data on political money spent by US firms, we reveal an unknown dichotomy. Firms taking a transactional approach to politics tend to use the least costly EM method, substituting accruals-based EM (AEM) for real EM (REM). Conversely, firms following a relational approach, concerned that possible detection may alienate career-focused politicians, substitute REM for AEM. Consistent with the goodwill trust in the firm–politicians relationship moderating the EM trade-off, firms revert to AEM when the trust is impaired and they no longer perceive the need to insulate politicians from reputational damage. Notwithstanding the firm’s political tactic, the total EM remains unaffected, suggesting perfect substitution. As a refined and dynamic lens for examining firm-politicians exchanges, our framework reconciles the conflicting evidence of prior studies on how political connections affect reported earnings and is generalizable to other third-party affiliations that may have important reputational stakes but no monitoring capacity over the production of financial information.Peer reviewe
‘I cannot be what I don’t see’ : an evaluation of Academic Intersectionality Mentoring in Medical Schools (AIMMS Mentoring)
Get PDFThe Academic Intersectionality Mentoring in Medical Schools (AIMMS Mentoring) scheme aims to support the career progression of women from ethnic minority backgrounds working in academic medicine and health sciences who are under-represented in senior roles of academia in the UK. Two questionnaires (baseline and 6 months) captured information about AIMMS Mentoring participants and practical aspects of the scheme. Participants were asked about their experience of and satisfaction with the scheme, whether it matched their expectations and what they felt were the scheme’s rewards and challenges. Questions were also asked about the organisation of the scheme and how it could be improved. The productivity of mentoring relationships was explored, including personal and professional development, and whether participants felt it important that mentoring takes place between people with similar characteristics. Sixteen pairs took part in mentoring, with ten mentees and four mentors completing evaluation questionnaires at 6m follow-up. Responses indicated that the scheme was helpful. All mentor and mentee responses reported personal and professional development. Mentee responses in particular reported gaining insight into career development, and both groups felt they had gained understanding about institutional ways of working. Participants rated the scheme positively and indicated they would recommend it to others. Being in mentoring relationships with women from similar backgrounds was ascribed value, as was mentor partners being empathetic. The evaluation revealed ways in which the scheme could be improved. Women from ethnic minorities working in academic medicine and health sciences can face structural barriers into leadership. This formative and summative evaluation of AIMMS Mentoring showed that mentoring and peer support in this group is valuable and can assist with personal, professional and career development. The scheme is an example of positive action and a model national activity aimed at achieving equity of opportunity in academic medicine and health sciences.Peer reviewe
Constraining the timing and climate forcing of the Long Island (Papua New Guinea) and Tarumae (Japan) eruptions and other 17th century volcanic eruptions
Get PDFFunding: Imogen Gabriel, Peter M. Abbott, and Michael Sigl received funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant number: 820047). Helen M. Innes and William Hutchison are funded by a UKRI Future Leaders Fellowship (grant number: MR/S033505/1). The St Andrews EPMA facility is supported by the EPSRC (grant numbers: EP/T019298/1, EP/L017008/1, EP/R023751/1). Jörg Franke was funded by the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant number: 787574). Collection and analysis of the Summit2023 core was supported by the US National Science Foundation (grant number: 2139293) to Nathan J. Chellman and Joseph R. McConnell. Development of the Greenland (Summit2015, TUNU2013, B19, NEEM-2011-S1) and Antarctic (WD, NUS, B40) continuous ice core sulfur and insoluble particle records was supported by the US National Science Foundation (grant numbers: 1406219, 1204176, 909541, 0538416, 0538427) to Joseph R. McConnell.The 17th century was a period when several major (VEI > 5) tropical and extratropical volcanic eruptions occurred. Amongst these is the VEI 6 eruption of Long Island (Papua New Guinea), which is suggested to have occurred between 1665 and 1668 CE based on historical accounts, radiocarbon dating constraints, and an ice-core record from South Pole. Accepting such an attribution on the basis of this ice-core chronology would imply a hitherto undiagnosed dating error of up to 6 years during the 17th century within all ice-core records from Antarctica. Here we constrain the timing of the Long Island eruption through tephrochronology and high-resolution glaciochemical measurements from an array of records from Antarctica and Greenland. We identify cryptotephra glass shards in association with the Greenland 1667 CE sulfate peak and geochemically attribute them to the historic Japanese Tarumae (Shikotsu) eruption. This attribution shows that the ice-core records are not misaligned during this period and refines the timing of the Long Island eruption to two candidate dates: 1654 ±1 CE and 1662 ±1 CE. Both candidate dates are within previous best age estimates based on radiocarbon dating (1651 and 1671 CE, 95.4 % probability). However, here we tentatively use 1662 ±1 CE as the timing of the Long Island eruption, as previous radiocarbon constraints suggest a 68.2 % probability of occurrence between 1655 and 1665 CE. With a higher confidence in the dating, we revised volcanic stratospheric sulfur injection (VSSI) estimates across the 17th century. Using these alongside paleo-proxy records, we explored the Northern Hemisphere climate response to the Long Island and Tarumae eruptions and found them to be more limited compared to other major (VEI >5) eruptions during this century. Ultimately, this study has highlighted the accuracy of ice core chronologies, having wider implications for volcanic forcing reconstructions and detection and attribution studies of natural climate variability.Peer reviewe
Shaping UK research priorities in the area of specific learning difficulties by surveying people with lived experience
Get PDFFunding: The SLDN (https://medicine.st-andrews.ac.uk/learning-difficulties/) was supported by an RSE workshop grant to SP and ML, and an MRC Harmonised IAA (MR/X502716/1) to SP. MM and RM were supported by the Biotechnology and Biological Sciences Research Council [BB/T000813/1].The specific learning difficulties (SpLD) network (SLDN) was established in 2022 to bring together UK researchers and stakeholders interested in SpLDs to better integrate research across different areas and to agree on research priorities. It was vital to include the views and experiences of people (and carers of children and young people) with SpLDs (here defined as dyslexia, dyscalculia, and dysgraphia) as part of the research priority-setting process. In this study, we analysed data from 145 participants (82 carers of a child or young person with an SpLD and 63 adults with an SpLD) from the UK (primary difficulty: 119 dyslexia, 14 dyscalculia, and 12 dysgraphia) on various issues around identification, labelling, support, mental health, and research priorities. Here, we present descriptive statistics separately for each SpLD where sample sizes permit. While not a population-representative survey, some key findings include: the high number of co-occurring SpLDs, high co-occurrence with other developmental traits, and high prevalence of mental health issues. Key priorities were around earlier identification and best ways to support SpLDs, and additionally, for dyscalculia, around increasing awareness. Suggestions for the next steps in the research priority-setting process include research based on co-production with people with lived experience of SpLD.Peer reviewe
The emission spectrum of the hot Jupiter WASP-79b from HST/WFC3
Get PDFFunding: G.B. acknowledges support from CHEOPS ASI-INAF agreement No. 2019-29-HH.0. This work has been carried out in the frame of the National Centre for Competence in Research PlanetS supported by the Swiss National Science Foundation (SNSF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project Spice Dune, grant agreement No. 947634).Here we present a thermal emission spectrum of WASP-79b, obtained via Hubble Space Telescope Wide Field Camera 3 G141 observations as part of the PanCET program. As we did not observe the ingress or egress of WASP-79b’s secondary eclipse, we consider two scenarios: a fixed mid-eclipse time based on the expected occurrence time, and a mid-eclipse time as a free parameter. In both scenarios, we can measure thermal emission from WASP-79b from 1.1 to 1.7 μm at 2.4σ confidence consistent with a 1900 K brightness temperature for the planet. We combine our observations with Spitzer dayside photometry (3.6 and 4.5 μm) and compare these observations to a grid of atmospheric forward models that span a range of metallicities, carbon-to-oxygen ratios, and recirculation factors. Given the strength of the planetary emission and the precision of our measurements, we found a wide range of forward models to be consistent with our data. The best-match equilibrium model suggests that WASP-79b’s dayside has a solar metallicity and carbon-to-oxygen ratio, alongside a recirculation factor of 0.75. Models including significant H− opacity provide the best match to WASP-79b’s emission spectrum near 1.58 μm. However, models featuring high-temperature cloud species—formed via vigorous vertical mixing and low sedimentation efficiencies—with little day-to-night energy transport also match WASP-79b’s emission spectrum. Given the broad range of equilibrium chemistry, disequilibrium chemistry, and cloudy atmospheric models consistent with our observations of WASP-79b’s dayside emission, further observations will be necessary to constrain WASP-79b’s dayside atmospheric properties.Peer reviewe
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