Ozone chemistry on tidally locked M dwarf planets

This is the final version. Available from Oxford University Press via the DOI in this recordWe use the Met Office Unified Model to explore the potential of a tidally locked M dwarf planet, nominally Proxima Centauri b irradiated by a quiescent version of its host star, to sustain an atmospheric ozone layer. We assume a slab ocean surface layer, and an Earth-like atmosphere of nitrogen and oxygen with trace amounts of ozone and water vapour. We describe ozone chemistry using the Chapman mechanism and the hydrogen oxide (HOx, describing the sum of OH and HO2) catalytic cycle. We find that Proxima Centauri radiates with sufficient UV energy to initialize the Chapman mechanism. The result is a thin but stable ozone layer that peaks at 0.75 parts per million at 25 km. The quasi-stationary distribution of atmospheric ozone is determined by photolysis driven by incoming stellar radiation and by atmospheric transport. Ozone mole fractions are smallest in the lowest 15 km of the atmosphere at the sub-stellar point and largest in the nightside gyres. Above 15 km the ozone distribution is dominated by an equatorial jet stream that circumnavigates the planet. The nightside ozone distribution is dominated by two cyclonic Rossby gyres that result in localized ozone hotspots. On the dayside the atmospheric lifetime is determined by the HOx catalytic cycle and deposition to the surface, with nightside lifetimes due to chemistry much longer than timescales associated with atmospheric transport. Surface UV values peak at the substellar point with values of 0.01 W/m2 , shielded by the overlying atmospheric ozone layer but more importantly by water vapour clouds.Leverhulme TrustScience and Technology Facilities Council (STFC

Using models of the Earth's atmosphere to assess exoplanet habitability

Recent advances in telescope technology have allowed us to detect planets and bodies that have the potential to be habitable. Habitability can be defined in a number of ways, but most commonly it is defined by the availability of liquid water. There are a vast number of factors that determine whether or not liquid water is present in an atmosphere or on a surface, and due to the limited observational data, our understanding of the role of each of these factors is poor, especially as we move further through the parameter space away from the Earth. Until data from the next generation of telescopes are available, attempts to constrain atmospheric habitability have to utilise computer modelling. Modelling has a long history in habitability studies, particularly with regards to the inner and outer boundaries of the circumstellar habitable zone (CHZ). Early models were 1-dimensional (1D), but in the last decade the balance has shifted towards 3-dimensional (3D) global circulation models (GCMs) that describe the air flow in a planetary atmosphere in a much more sophisticated way. In part this was due to the recognition of the importance of 3D processes like clouds and convection in the global energy balance, and in part due to the increasing prioritisation of planets that are dissimilar to Earth, such as M-dwarf planets, which show features such as tidal-locking and atmospheric jets that result in less spatial uniformity through the atmosphere, limiting the applicability of 1D models. As of this writing our current best hopes for habitability are M-dwarf planets such as the TRAPPIST planets and Proxima Centauri b that orbit in the habitable zone, with rocky compositions. M-dwarf planets were previously overlooked as candidate habitable planets in favour of G-star planets like the Earth. However, some researchers now favour M-dwarfs in light of modern GCM results, observational biases and planetary population statistics, demonstrating that we must be careful not to define habitability in a way that is too Earth-centric. In this thesis we expand on knowledge of habitability through models that are informed by Earth science, but that do not necessarily describe Earth-like environments. In Chapter 2, we consider an environment that has not been studied through the lens of habitability before: ultra-cool Y dwarf atmospheres. In the atmospheres of these bodies it is thought that there may be liquid water clouds and temperatures and pressures similar to those on the Earth's surface. However, as there is no surface it is important that any potential organisms are able to remain above the hot lower atmosphere and the cold upper atmosphere; we compare with the Earth's atmosphere, where microbes are able to stay in the atmosphere for weeks, even metabolising in clouds. We study this environment through a simple radiative or convective atmosphere paired with a model informed by nutrient-phytoplankton-zooplankton models from the Earth's ocean. We find that organisms similar in size to microbes can remain aloft in this environment due to upward convective winds. In Chapter 3, contrasting with the simple approach in the previous chapter, we describe the development of a highly-sophisticated, fully online, 3D photochemical model of an exoplanet atmosphere. We apply this model to a tidally-locked M-dwarf aqua planet with an Earth-like atmosphere, nominally Proxima Centauri b, to evaluate the impacts of the differing stellar energy spectrum and dramatically different global circulation on an ozone layer described through the Chapman mechanism and the hydrogen oxide catalytic cycle. We find that the ozone layer is unlike that seen in the Earth's atmosphere. The lack of UV photons from our quiescent M-dwarf results in very long chemical lifetimes, which means that the atmospheric transport becomes the dominant factor in the structure of the ozone layer. We see an accumulation of ozone in the night-side cold traps (or gyres) at low altitudes where transport is slow and lifetimes are long, resulting in a dramatic day-night contrast in ozone columns. Total ozone column is much smaller on an M-dwarf planet compared with the Earth, by around a factor of 10, owing to top-of-atmosphere UV flux. In Chapter 4, we develop on the results of Chapter 3 by altering certain parameters in the model and examining the effect on the climate. We find that dramatic changes occur when switching off the chemistry scheme and reverting to a prescribed Earth ozone layer. Specifically we find that the temperatures on the night side of the planet change by more than 50 K, accompanied by dramatic changes in the pole temperatures. In addition the cold traps move towards the equator and eastwards. These changes are caused by the smaller ozone columns that result from the interactive chemistry, which severely reduce night side atmosphere opacity. This opacity controls the night side cooling rate which in turn controls the atmospheric circulation through the day-tonight temperature contrast. We find that similar effects occur when switching off the hydrogen oxide catalytic loss cycle, though to a lesser extent. Furthermore, we examine the effects of electromagnetic flares on the chemistry, which do not seem to impact ozone columns, in agreement with previous works. Finally we demonstrate the changes in atmospheric ozone and climate in a 3:2 resonant orbit and with an Earth-like orbit and top-of-atmosphere flux. In sum, our results with this model show that the climate is highly sensitive to the ozone columns, and demonstrate the importance of fully-coupled 3D photochemical models, which have been used very rarely in exoplanet atmosphere modelling

Treatment strategies for progressive immune effector cell-associated hemophagocytic lymphohistiocytosis-like syndrome: case series

Not available

Processed pseudogenes acquired somatically during cancer development.

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5' truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

The Biomolecular Interaction Network Database and related tools 2005 update

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues

Toward community standards in the quest for orthologs

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: [email protected]

Therapeutic Validity and Effectiveness of Preoperative Exercise on Functional Recovery after Joint Replacement: A Systematic Review and Meta-Analysis

Background: Our aim was to develop a rating scale to assess the therapeutic validity of therapeutic exercise programmes. By use of this rating scale we investigated the therapeutic validity of therapeutic exercise in patients awaiting primary total joint replacement (TJR). Finally, we studied the association between therapeutic validity of preoperative therapeutic exercise and its effectiveness in terms of postoperative functional recovery. Methods: (Quasi) randomised clinical trials on preoperative therapeutic exercise in adults awaiting TJR on postoperative recovery of functioning within three months after surgery were identified through database and reference screening. Two reviewers extracted data and assessed the risk of bias and therapeutic validity. Therapeutic validity of the interventions was assessed with a nine-itemed, expert-based rating scale (scores range from 0 to 9; score ≥6 reflecting therapeutic validity), developed in a four-round Delphi study. Effects were pooled using a random-effects model and meta-regression was used to study the influence of therapeutic validity. Results: Of the 7,492 articles retrieved, 12 studies (737 patients) were included. None of the included studies demonstrated therapeutic validity and two demonstrated low risk of bias. Therapeutic exercise was not associated with 1) observed functional recovery during the hospital stay (Standardised Mean Difference [SMD]: −1.19; 95%-confidence interval [CI], −2.46 to 0.08); 2) observed recovery within three months of surgery (SMD: −0.15; 95%-CI, −0.42 to 0.12); and 3) self-reported recovery within three months of surgery (SMD −0.07; 95%-CI, −0.35 to 0.21) compared with control participants. Meta-regression showed no statistically significant relationship between therapeutic validity and pooled-effects. Conclusion: Preoperative therapeutic exercise for TJR did not demonstrate beneficial effects on postoperative functional recovery. However, poor therapeutic validity of the therapeutic exercise programmes may have hampered potentially beneficial effects, since none of the studies met the predetermined quality criteria. Future review studies on therapeutic exercise should address therapeutic validity. (aut.ref.

Gradients of anthropogenic nutrient enrichment alter N Composition and DOM stoichiometry in freshwater ecosystems

Plain language summary Ammonium and nitrate in freshwaters have received considerable attention due to their clear ecological and health effects. A comprehensive assessment of N in freshwaters that includes DON is lacking. Including DON in studies of surface water chemistry is important because it can cause eutrophication and certain forms can be rapidly removed by microbial communities. Here, we document how elevated levels of TDN impact the concentrations and relative proportions of all three forms of dissolved N and the stoichiometry of DOM. Our results suggest that human activities fundamentally alter the composition of the dissolved nitrogen pool and the stoichiometry of DOM. Results also highlight feedbacks between the C and N cycles in freshwater ecosystems that are poorly studied.A comprehensive cross-biome assessment of major nitrogen (N) species that includes dissolved organic N (DON) is central to understanding interactions between inorganic nutrients and organic matter in running waters. Here, we synthesize stream water N chemistry across biomes and find that the composition of the dissolved N pool shifts from highly heterogeneous to primarily comprised of inorganic N, in tandem with dissolved organic matter (DOM) becoming more N-rich, in response to nutrient enrichment from human disturbances. We identify two critical thresholds of total dissolved N (TDN) concentrations where the proportions of organic and inorganic N shift. With low TDN concentrations (0–1.3 mg/L N), the dominant form of N is highly variable, and DON ranges from 0% to 100% of TDN. At TDN concentrations above 2.8 mg/L, inorganic N dominates the N pool and DON rarely exceeds 25% of TDN. This transition to inorganic N dominance coincides with a shift in the stoichiometry of the DOM pool, where DOM becomes progressively enriched in N and DON concentrations are less tightly associated with concentrations of dissolved organic carbon (DOC). This shift in DOM stoichiometry (defined as DOC:DON ratios) suggests that fundamental changes in the biogeochemical cycles of C and N in freshwater ecosystems are occurring across the globe as human activity alters inorganic N and DOM sources and availability. Alterations to DOM stoichiometry are likely to have important implications for both the fate of DOM and its role as a source of N as it is transported downstream to the coastal ocean

Processed pseudogenes acquired somatically during cancer development

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context