Ocean ecosystems are increasingly stressed by human-induced changes of their physical, chemical and biological environment. Among these changes, warming, acidification, deoxygenation and changes in ...primary productivity by marine phytoplankton can be considered as four of the major stressors of open ocean ecosystems. Due to rising atmospheric CO2 in the coming decades, these changes will be amplified. Here, we use the most recent simulations performed in the framework of the Coupled Model Intercomparison Project 5 to assess how these stressors may evolve over the course of the 21st century. The 10 Earth system models used here project similar trends in ocean warming, acidification, deoxygenation and reduced primary productivity for each of the IPCC's representative concentration pathways (RCPs) over the 21st century. For the "business-as-usual" scenario RCP8.5, the model-mean changes in the 2090s (compared to the 1990s) for sea surface temperature, sea surface pH, global O2 content and integrated primary productivity amount to +2.73 (±0.72) °C, −0.33 (±0.003) pH unit, −3.45 (±0.44)% and −8.6 (±7.9)%, respectively. For the high mitigation scenario RCP2.6, corresponding changes are +0.71 (±0.45) °C, −0.07 (±0.001) pH unit, −1.81 (±0.31)% and −2.0 (±4.1)%, respectively, illustrating the effectiveness of extreme mitigation strategies. Although these stressors operate globally, they display distinct regional patterns and thus do not change coincidentally. Large decreases in O2 and in pH are simulated in global ocean intermediate and mode waters, whereas large reductions in primary production are simulated in the tropics and in the North Atlantic. Although temperature and pH projections are robust across models, the same does not hold for projections of subsurface O2 concentrations in the tropics and global and regional changes in net primary productivity. These high uncertainties in projections of primary productivity and subsurface oxygen prompt us to continue inter-model comparisons to understand these model differences, while calling for caution when using the CMIP5 models to force regional impact models.
Nicotinic acetylcholine receptors play important roles in numerous cognitive processes as well as in several debilitating central nervous system (CNS) disorders. In order to fully elucidate the ...diverse roles of nicotinic acetylcholine receptors in CNS function and dysfunction, a detailed knowledge of their cellular and subcellular localizations is essential. To date, methods to precisely localize nicotinic acetylcholine receptors in the CNS have predominantly relied on the use of anti-receptor subunit antibodies. Although data obtained by immunohistology and immunoblotting are generally in accordance with ligand binding studies, some discrepancies remain, in particular with electrophysiological findings. In this context, nicotinic acetylcholine receptor subunit-deficient mice should be ideal tools for testing the specificity of subunit-directed antibodies. Here, we used standard protocols for immunohistochemistry and western blotting to examine the antibodies raised against the α3-, α4-, α7-, β2-, and β4-nicotinic acetylcholine receptor subunits on brain tissues of the respective knock-out mice. Unexpectedly, for each of the antibodies tested, immunoreactivity was the same in wild-type and knock-out mice. These data imply that, under commonly used conditions, these antibodies are not suited for immunolocalization. Thus, particular caution should be exerted with regards to the experimental approach used to visualize nicotinic acetylcholine receptors in the brain.
The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search ...for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic "nematophytes" have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.
Marine scientists often use two measured or modeled carbonate system variables to compute others. These carbonate chemistry calculations, based on well-known thermodynamic equilibria, are now ...available in a dozen public packages. Ten of those were compared using common input data and the set of equilibrium constants recommended for best practices. Current versions of all 10 packages agree within 0.2 μatm for pCO2, 0.0002 units for pH, and 0.1 μmol kg−1 for CO32− in terms of surface zonal-mean values. That represents more than a 10-fold improvement relative to outdated versions of the same packages. Differences between packages grow with depth for some computed variables but remain small. Discrepancies derive largely from differences in equilibrium constants. Analysis of the sensitivity of each computed variable to changes in each constant reveals the general dominance of K1 and K2 but also the comparable sensitivity to KB for the AT–CT input pair. Best-practice formulations for K1 and K2 are implemented consistently among packages. Yet with more recent formulations designed to cover a wider range of salinity, packages disagree by up to 8 μatm in pCO2, 0.006 units in pH, and 1 μmol kg−1 in CO32− under typical surface conditions. They use different proposed sets of coefficients for these formulations, all of which are inconsistent. Users would do well to use up-to-date versions of packages and the constants recommended for best practices.
Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and ...adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE–MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.
•Collaboration and conflict between MGEs can promote and inhibit HGT•Many genome defences are MGE-encoded, serving MGE interests and changing frequently•The presence of multiple MGEs in a cell presents new opportunities for HGT•MGE–MGE conflict is often multilayered and dynamic, with shifting allegiances
New approaches for the sensitive and accurate quantification of aerosol optical properties are needed to improve the current understanding of the unique physical chemistry of airborne particles and ...to explore their roles in fields as diverse as chemical manufacturing, healthcare, and atmospheric science. We have pioneered the use of cavity ring-down spectroscopy (CRDS), with concurrent angularly resolved elastic light scattering measurements, to interrogate the optical properties of single aerosol particles levitated in optical and electrodynamic traps. This approach enables the robust quantification of optical properties such as extinction cross sections for individual particles of known size. Our measurements can now distinguish the scattering and absorption contributions to the overall light extinction, from which the real and imaginary components of the complex refractive indices can be retrieved and linked to chemical composition. In this Feature Article, we show that this innovative measurement platform enables accurate and precise optical measurements for spherical and nonspherical particles, whether nonabsorbing or absorbing at the CRDS probe wavelength. We discuss the current limitations of our approach and the key challenges in physical and atmospheric chemistry that can now be addressed by CRDS measurements for single aerosol particles levitated in controlled environments.
This paper presents a summary of the measurements made during the heavily-instrumented Reactive Halogens in the Marine Boundary Layer (RHaMBLe) coastal study in Roscoff on the North West coast of ...France throughout September 2006. It was clearly demonstrated that iodine-mediated coastal particle formation occurs, driven by daytime low tide emission of molecular iodine, I2, by macroalgal species fully or partially exposed by the receding waterline. Ultrafine particle concentrations strongly correlate with the rapidly recycled reactive iodine species, IO, produced at high concentrations following photolysis of I2. The heterogeneous macroalgal I2 sources lead to variable relative concentrations of iodine species observed by path-integrated and in situ measurement techniques. Apparent particle emission fluxes were associated with an enhanced apparent depositional flux of ozone, consistent with both a direct O3 deposition to macroalgae and involvement of O3 in iodine photochemistry and subsequent particle formation below the measurement height. The magnitude of the particle formation events was observed to be greatest at the lowest tides with the highest concentrations of ultrafine particles growing to the largest sizes, probably by the condensation of anthropogenically-formed condensable material. At such sizes the particles should be able to act as cloud condensation nuclei at reasonable atmospheric supersaturations.
It is widely accepted that climate change poses severe threats to freshwater ecosystems. Here we examine the scientific basis for adaptively managing vulnerable habitats and species. Our views are ...shaped by a literature survey of adaptation in practice, and by expert opinion. We assert that adaptation planning is constrained by uncertainty about evolving climatic and non-climatic pressures, by difficulties in predicting species- and ecosystem-level responses to these forces, and by the plasticity of management goals. This implies that adaptation measures will have greatest acceptance when they deliver multiple benefits, including, but not limited to, the amelioration of climate impacts. We suggest that many principles for biodiversity management under climate change are intuitively correct but hard to apply in practice. This view is tested using two commonly assumed doctrines: “increase shading of vulnerable reaches through tree planting” (to reduce water temperatures); and “set hands off flows” (to halt potentially harmful abstractions during low flow episodes). We show that the value of riparian trees for shading, water cooling and other functions is partially understood, but extension of this knowledge to water temperature management is so far lacking. Likewise, there is a long history of environmental flow assessment for allocating water to competing uses, but more research is needed into the effectiveness of ecological objectives based on target flows. We therefore advocate more multi-disciplinary field and model experimentation to test the cost-effectiveness and efficacy of adaptation measures applied at different scales. In particular, there is a need for a major collaborative programme to: examine natural adaptation to climatic variation in freshwater species; identify where existing environmental practice may be insufficient; review the fitness of monitoring networks to detect change; translate existing knowledge into guidance; and implement best practice within existing regulatory frameworks.
Abstract
STUDY QUESTION
Does incisional endometriosis (IE) harbor somatic cancer-driver mutations?
SUMMARY ANSWER
We found that approximately one-quarter of IE cases harbor somatic-cancer mutations, ...which commonly affect components of the MAPK/RAS or PI3K-Akt-mTor signaling pathways.
WHAT IS KNOWN ALREADY
Despite the classification of endometriosis as a benign gynecological disease, it shares key features with cancers such as resistance to apoptosis and stimulation of angiogenesis and is well-established as the precursor of clear cell and endometrioid ovarian carcinomas. Our group has recently shown that deep infiltrating endometriosis (DE), a form of endometriosis that rarely undergoes malignant transformation, harbors recurrent somatic mutations.
STUDY DESIGN, SIZE, DURATION
In a retrospective study comparing iatrogenically induced and endogenously occurring forms of endometriosis unlikely to progress to cancer, we examined endometriosis specimens from 40 women with IE and 36 women with DE. Specimens were collected between 2004 and 2017 from five hospital sites in either Canada, Germany or the Netherlands. IE and DE cohorts were age-matched and all women presented with histologically typical endometriosis without known history of malignancy.
PARTICIPANTS/MATERIALS, SETTING, METHODS
Archival tissue specimens containing endometriotic lesions were macrodissected and/or laser-capture microdissected to enrich endometriotic stroma and epithelium and a hypersensitive cancer hotspot sequencing panel was used to assess for presence of somatic mutations. Mutations were subsequently validated using droplet digital PCR. PTEN and ARID1A immunohistochemistry (IHC) were performed as surrogates for somatic events resulting in functional loss of respective proteins.
MAIN RESULTS AND THE ROLE OF CHANCE
Overall, we detected somatic cancer-driver events in 11 of 40 (27.5%) IE cases and 13 of 36 (36.1%) DE cases, including hotspot mutations in KRAS, ERBB2, PIK3CA and CTNNB1. Heterogeneous PTEN loss occurred at similar rates in IE and DE (7/40 vs 5/36, respectively), whereas ARID1A loss only occurred in a single case of DE. While rates of detectable somatic cancer-driver events between IE and DE are not statistically significant (P > 0.05), KRAS activating mutations were more prevalent in DE.
LIMITATIONS, REASONS FOR CAUTION
Detection of somatic cancer-driver events were limited to hotspots analyzed in our panel-based sequencing assay and loss of protein expression by IHC from archival tissue. Whole genome or exome sequencing, or epigenetic analysis may uncover additional somatic alterations. Moreover, because of the descriptive nature of this study, the functional roles of identified mutations within the context of endometriosis remain unclear and causality cannot be established.
WIDER IMPLICATIONS OF THE FINDINGS
The alterations we report may be important in driving the growth and survival of endometriosis in ectopic regions of the body. Given the frequency of mutation in surgically displaced endometrium (IE), examination of similar somatic events in eutopic endometrium, as well as clinically annotated cases of other forms of endometriosis, in particular endometriomas that are most commonly linked to malignancy, is warranted.
STUDY FUNDING/COMPETING INTEREST(S)
This study was funded by a Canadian Cancer Society Impact Grant 701603, PI Huntsman, Canadian Institutes of Health Research Transitional Open Operating Grant MOP-142273, PI Yong, the Canadian Institutes of Health Research Foundation Grant FDN-154290, PI Huntsman, the Canadian Institutes of Health Research Project Grant PJT-156084, PIs Yong and Anglesio, and the Janet D. Cottrelle Foundation through the BC Cancer Foundation PI Huntsman. D.G. Huntsman is a co-founder and shareholder of Contextual Genomics Inc., a for profit company that provides clinical reporting to assist in cancer patient treatment. R. Aguirre-Hernandez, J. Khattra and L.M. Prentice have a patent MOLECULAR QUALITY ASSURANCE METHODS FOR USE IN SEQUENCING pending and are current (or former) employees of Contextual Genomics Inc. The remaining authors have no competing interests to declare.
TRIAL REGISTRATION NUMBER
Not applicable.
The occurrence of surface melt in Antarctica has hitherto been associated with the austral summer season, when the dominant source of melt energy is provided by solar radiation. We use in situ and ...satellite observations from a previously unsurveyed region to show that events of intense surface melt on Larsen C Ice Shelf occur frequently throughout the dark Antarctic winter, with peak intensities sometimes exceeding summertime values. A regional atmospheric model confirms that in the absence of solar radiation, these multiday melt events are driven by outbreaks of warm and dry föhn wind descending down the leeside of the Antarctic Peninsula mountain range, resulting in downward turbulent fluxes of sensible heat that drive sustained surface melt fluxes in excess of 200 W/m2. From 2015 to 2017 (including the extreme melt winter of 2016), ∼23% of the annual melt flux was produced in winter, and spaceborne observations of surface melt since 2000 show that wintertime melt is widespread in some years. Winter melt heats the firn layer to the melting point up to a depth of ∼3 m, thereby facilitating the formation of impenetrable ice layers and retarding or reversing autumn and winter cooling of the firn. While the absence of a trend in winter melt is consistent with insignificant changes in the observed Southern Hemisphere atmospheric circulation during winter, we anticipate an increase in winter melt as a response to increasing greenhouse gas concentration.
Plain Language Summary
Around the coast of Antarctica, it gets warm enough in summer for snow to start melting, and the sun provides most of the energy for that melt. Almost all meltwater refreezes in the snowpack, but especially on floating glaciers in Antarctica, it has been observed that meltwater forms large ponds. The pressure exerted by these ponds may have led to ice shelves collapsing into numerous icebergs in recent decades. It is therefore important to understand how much meltwater is formed. To find out, we installed an automatic weather station on a glacier in Cabinet Inlet, in the Antarctic Peninsula in 2014. The station recorded temperatures well above the melting point even in winter. The occurrence of winter melt is confirmed by satellite images and by thermometers buried in the snow, which measured a warming of the snow even at 3 m depth. Between 2014 and 2017, about 23% of all melt in Cabinet Inlet occurred in winter. Winter melt is due to warm winds that descend from the mountains, known as föhn. We have not seen the amount of winter melt increasing since 2000. However, we expect winter melt to happen more frequently if greenhouse gas continues to accumulate in the atmosphere.
Key Points
Wintertime surface melt occurs frequently in the Antarctic Peninsula
Winter melt heats the firn to a depth of about 3 m, retarding or reversing winter cooling
Increased greenhouse gas concentrations could increase the occurrence of winter surface melt
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