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Diamond, Michael S.

Publications and source records attributed to Diamond, Michael S..

11 records
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DOE OSTI2024

Computationally restoring the potency of a clinical antibody against Omicron

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs and revealed how quickly viral escape can curtail effective options. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A compendium of multi-omics data illuminating host responses to lethal human virus infections

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Physical science research needed to evaluate the viability and risks of marine cloud brightening

Marine cloud brightening (MCB) is the deliberate injection of aerosol particles into shallow marine clouds to increase their reflection of solar radiation and reduce the amount of energy absorbed by the climate system. From the physical science perspective, the consensus of a broad international group of scientists is that the viability of MCB will ultimately depend on whether observations and models can robustly assess the scale-up of local-to-global brightening in today’s climate and identify strategies that will ensure an equitable geographical distribution of the benefits and risks associated with projected regional changes in temperature and precipitation. To address the physical science knowledge gaps required to assess the societal implications of MCB, we propose a substantial and targeted program of research—field and laboratory experiments, monitoring, and numerical modeling across a range of scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

DOE-NOAA Marine Cloud Brightening (Workshop Report 2022)

Marine Cloud Brightening (MCB) refers to the deliberate injection of aerosol particles into marine clouds to increase their reflection of solar radiation to temporarily cool the planet while decarbonization efforts are pursued. A workshop was conducted to assess the state of knowledge in the field of MCB, and to provide a possible research path toward reducing unknowns in key components of the underlying physical science. This three-day workshop took place in April 2022 and was jointly sponsored by Department of Energy (DOE)’s Atmospheric System Research (ASR) program and the National Oceanic and Atmospheric Administration (NOAA). The workshop focused on identifying key physical science knowledge gaps necessary to answer the following driving questions: 1) Is MCB feasible over sufficiently large regions and is implementation practicable for long-enough durations to avert the worst impacts of global warming? 2) If practicable, what will be the regional impacts of such MCB interventions? 3) Do we have adequate systems in place to detect and quantify the effects of such interventions? 4) What physical and engineering science challenges must be resolved satisfactorily before we can consider embarking on MCB?

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Cloud adjustments from large-scale smoke–circulation interactions strongly modulate the southeastern Atlantic stratocumulus-to-cumulus transition

Smoke from southern Africa blankets the southeastern Atlantic Ocean from June to October, producing strong and competing aerosol radiative effects. Smoke effects on the transition between overcast stratocumulus and scattered cumulus clouds are investigated along a Lagrangian (air-mass-following) trajectory in regional climate and large eddy simulation models. Results are compared with observations from three recent field campaigns that took place in August 2017: ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES), CLouds and Aerosol Radiative Impacts and Forcing: Year 2017 (CLARIFY), and Layered Atlantic Smoke Interactions with Clouds (LASIC). The case study is set up around the joint ORACLES–CLARIFY flight that took place near Ascension Island on 18 August 2017. Smoke sampled upstream on an ORACLES flight on 15 August 2017 likely entrained into the marine boundary layer later sampled during the joint flight. The case is first simulated with the WRF-CAM5 regional climate model in three distinct setups: (1) FireOn, in which smoke emissions and any resulting smoke–cloud–radiation interactions are included; (2) FireOff, in which no smoke emissions are included; (3) RadOff, in which smoke emissions and their microphysical effects are included but aerosol does not interact directly with radiation. Over the course of the Lagrangian trajectory, differences in free tropospheric thermodynamic properties between FireOn and FireOff are nearly identical to those between FireOn and RadOff, showing that aerosol–radiation interactions are primarily responsible for the free tropospheric effects. These effects are non-intuitive: in addition to the expected heating within the core of the smoke plume, there is also a “banding” effect of cooler temperature (~1–2 K) and greatly enhanced moisture (>2 g kg -1 ) at the plume top. This banding effect is caused by a vertical displacement of the former continental boundary layer in the free troposphere in the FireOn simulation resulting from anomalous diabatic heating due to smoke absorption of sunlight that manifests primarily as a few hundred meters per day reduction in large-scale subsidence over the ocean. A large eddy simulation (LES) is then forced with free tropospheric fields taken from the outputs for the WRF-CAM5 FireOn and FireOff runs. Cases are run by selectively perturbing one variable (e.g., aerosol number concentration, temperature, moisture, vertical velocity) at a time to better understand the contributions from different indirect (microphysical), “large-scale” semi-direct (above-cloud thermodynamic and subsidence changes), and “local” semi-direct (below-cloud smoke absorption) effects. Despite a more than 5-fold increase in cloud droplet number concentration when including smoke aerosol concentrations, minimal differences in cloud fraction evolution are simulated by the LES when comparing the base case with a perturbed aerosol case with identical thermodynamic and dynamic forcings. A factor of 2 decrease in background free tropospheric aerosol concentrations from the FireOff simulation shifts the cloud evolution from a classical entrainment-driven “deepening–warming” transition to trade cumulus to a precipitation-driven “drizzle-depletion” transition to open cells, however. The thermodynamic and dynamic changes caused by the WRF-simulated large-scale adjustments to smoke diabatic heating strongly influence cloud evolution in terms of both the rate of deepening (especially for changes in the inversion temperature jump and in subsidence) and in cloud fraction on the final day of the simulation (especially for the moisture “banding” effect). Such large-scale semi-direct effects would not have been possible to simulate using a small-domain LES model alone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗
DOE OSTI2021

An overview of the ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) project: aerosol–cloud–radiation interactions in the southeast Atlantic basin

Southern Africa produces almost a third of the Earth's biomass burning (BB) aerosol particles, yet the fate of these particles and their influence on regional and global climate is poorly understood. ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) is a 5-year NASA EVS-2 (Earth Venture Suborbital-2) investigation with three intensive observation periods designed to study key atmospheric processes that determine the climate impacts of these aerosols. During the Southern Hemisphere winter and spring (June-October), aerosol particles reaching 3-5 km in altitude are transported westward over the southeast Atlantic, where they interact with one of the largest subtropical stratocumulus (Sc) cloud decks in the world. The representation of these interactions in climate models remains highly uncertain in part due to a scarcity of observational constraints on aerosol and cloud properties, as well as due to the parameterized treatment of physical processes. Three ORACLES deployments by the NASA P-3 aircraft in September 2016, August 2017, and October 2018 (totaling ~350 science flight hours), augmented by the deployment of the NASA ER-2 aircraft for remote sensing in September 2016 (totaling ~100 science flight hours), were intended to help fill this observational gap. ORACLES focuses on three fundamental science themes centered on the climate effects of African BB aerosols: (a) direct aerosol radiative effects, (b) effects of aerosol absorption on atmospheric circulation and clouds, and (c) aerosol–cloud microphysical interactions. This paper summarizes the ORACLES science objectives, describes the project implementation, provides an overview of the flights and measurements in each deployment, and highlights the integrative modeling efforts from cloud to global scales to address science objectives. Significant new findings on the vertical structure of BB aerosol physical and chemical properties, chemical aging, cloud condensation nuclei, rain and precipitation statistics, and aerosol indirect effects are emphasized, but their detailed descriptions are the subject of separate publications. The main purpose of this paper is to familiarize the broader scientific community with the ORACLES project and the dataset it produced.

54 ENVIRONMENTAL SCIENCES↗