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Molecular optimization using a conditional transformer for reaction-aware compound exploration with reinforcement learning
Designing molecules with desirable properties is a critical endeavor in drug discovery. Because of recent advances in deep learning, molecular generative models have been developed. However, the existing compound exploration models often disregard the important issue of ensuring the feasibility of organic synthesis. To address this issue, we propose TRACER, which is a framework that integrates the optimization of molecular property optimization with synthetic pathway generation. The model can predict the product derived from a given reactant via a conditional transformer under the constraints of a reaction type. The molecular optimization results of an activity prediction model targeting DRD2, AKT1, and CXCR4 revealed that TRACER effectively generated compounds with high scores. The transformer model, which recognizes the entire structures, captures the complexity of the organic synthesis and enables its navigation in a vast chemical space while considering real-world reactivity constraints.
Anthropogenic organic aerosol in Europe produced mainly through second-generation oxidation
Exposure to anthropogenic atmospheric aerosol is a major health issue, causing several million deaths per year worldwide. The oxidation of aromatic hydrocarbons from traffic and wood combustion is an important anthropogenic source of low-volatility species in secondary organic aerosol, especially in heavily polluted environments. It is not yet established whether the formation of anthropogenic secondary organic aerosol involves mainly rapid autoxidation, slower sequential oxidation steps or a combination of the two. Here we reproduced a typical urban haze in the ‘Cosmics Leaving Outdoor Droplets’ chamber at the European Organization for Nuclear Research and observed the dynamics of aromatic oxidation products during secondary organic aerosol growth on a molecular level to determine mechanisms underlying their production and removal. We demonstrate that sequential oxidation is required for substantial secondary organic aerosol formation. Second-generation oxidation decreases the products’ saturation vapour pressure by several orders of magnitude and increases the aromatic secondary organic aerosol yields from a few percent to a few tens of percent at typical atmospheric concentrations. Through regional modelling, we show that more than 70% of the exposure to anthropogenic organic aerosol in Europe arises from second-generation oxidation.
Rapid rise in atmospheric CO2 marked the end of the Late Palaeozoic Ice Age
Atmospheric CO2 is thought to play a fundamental role in Earth’s climate regulation. Yet, for much of Earth’s geological past, atmospheric CO2 has been poorly constrained, hindering our understanding of transitions between cool and warm climates. Beginning ~370 million years ago in the Late Devonian and ending ~260 million years ago in the Permian, the Late Palaeozoic Ice Age was the last major glaciation preceding the current Late Cenozoic Ice Age and possibly the most intense glaciation witnessed by complex lifeforms. From the onset of the main phase of the Late Palaeozoic Ice Age in the mid-Mississippian ~330 million years ago, the Earth is thought to have sustained glacial conditions, with continental ice accumulating in high to mid-latitudes. Here we present an 80-million-year-long boron isotope record within a proxy framework for robust quantification of CO2. Our record reveals that the main phase of the Late Palaeozoic Ice Age glaciation was maintained by prolonged low CO2, unprecedented in Earth’s history. About 294 million years ago, atmospheric CO2 rose abruptly (4-fold), releasing the Earth from its penultimate ice age and transforming the Early Permian into a warmer world.
Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria
Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODHMs (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site—likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink—indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
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