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  1. Abstract Background

    Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH — an important global coral reef stressor — can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome.

    Results

    We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation.

    Conclusions

    We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem change.

     
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  2. Free, publicly-accessible full text available October 1, 2024
  3. Abstract

    Global warming is expected to cause significant changes in the pattern of precipitation minus evaporation (PE), which represents the net flux of water from the atmosphere to the surface or, equivalently, the convergence of moisture transport within the atmosphere. In most global climate model simulations, the pattern ofPEchange resembles an amplification of the historical pattern—a tendency known as “wet gets wetter, dry gets drier.” However, models also predict significant departures from this approximation that are not well understood. Here, we introduce a new method of decomposing the pattern ofPEchange into contributions from various dynamic and thermodynamic mechanisms and use it to investigate the response ofPEto global warming within the CESM1 Large Ensemble. In contrast to previous decompositions ofPEchange, ours incorporates changes not only in the monthly means of atmospheric winds and moisture, but also in their temporal variability, allowing us to isolate the hydrologic impacts of changes in the mean circulation, transient eddies, relative humidity, and the spatial and temporal distributions of temperature. In general, we find that changes in the mean circulation primarily control thePEresponse in the tropics, while temperature changes dominate at higher latitudes. Although the relative importance of specific mechanisms varies by region, at the global scale departures from the wet-gets-wetter approximation over land are primarily due to changes in the temperature lapse rate, while changes in the mean circulation, relative humidity, and horizontal temperature gradients play a secondary role.

     
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  4. Abstract

    Measuring local polar ordering is key to understanding ferroelectricity in thin films, especially for systems with small domains or significant disorder. Scanning nanobeam electron diffraction (NBED) provides an effective local probe of lattice parameters, local fields, polarization directions, and charge densities, which can be analyzed using a relatively low beam dose over large fields of view. However, quantitatively extracting the magnitudes and directions of polarization vectors from NBED remains challenging. Here, we use a cepstral approach, similar to a pair distribution function, to determine local polar displacements that drive ferroelectricity from NBED patterns. Because polar distortions generate asymmetry in the diffraction pattern intensity, we can efficiently recover the underlying displacements from the imaginary part of the cepstrum transform. We investigate the limits of this technique using analytical and simulated data and give experimental examples, achieving the order of 1.1 pm precision and mapping of polar displacements with nanometer resolution.

     
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    Free, publicly-accessible full text available July 12, 2024
  5. Free, publicly-accessible full text available May 11, 2024
  6. Abstract

    Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture ‘structural surfaceomics’. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.

     
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