Coupled atmospheric chemistry, radiation, and dynamics of an exoplanet generate self-sustained oscillations.

Nonlinearity in photochemical systems is known to allow self-sustained oscillations, but they have received little attention in studies of planetary atmospheres. Here, we present a unique, self-oscillatory solution for ozone chemistry of an exoplanet from a numerical simulation using a fully coupled, three-dimensional (3D) atmospheric chemistry-radiation-dynamics model. Forced with nonvarying stellar insolation and emission flux of nitric oxide (NO), atmospheric ozone abundance oscillates by a factor of thirty over a multidecadal timescale. As such self-oscillations can only occur with biological nitrogen fixation contributing to NO emission, we propose that they are a unique class of biosignature. The resulting temporal variability in the atmospheric spectrum is potentially observable. Our results underscore the importance of revisiting the spectra of exoplanets over multidecadal timescales to characterizing the atmospheric chemistry of exoplanets and searching for exoplanet biosignatures. There are also profound implications for comparative planetology and the evolution of the atmospheres of terrestrial planets in the solar system and beyond. Fully coupled, 3D atmospheric chemistry-radiation-dynamics models can reveal new phenomena that may not exist in one-dimensional models, and hence, they are powerful tools for future planetary atmospheric research.

From COVID-19 to future electrification: Assessing traffic impacts on air quality by a machine-learning model.

The large fluctuations in traffic during the COVID-19 pandemic provide an unparalleled opportunity to assess vehicle emission control efficacy. Here we develop a random-forest regression model, based on the large volume of real-time observational data during COVID-19, to predict surface-level NO2, O3, and fine particle concentration in the Los Angeles megacity. Our model exhibits high fidelity in reproducing pollutant concentrations in the Los Angeles Basin and identifies major factors controlling each species. During the strictest lockdown period, traffic reduction led to decreases in NO2 and particulate matter with aerodynamic diameters <2.5 µm by -30.1% and -17.5%, respectively, but a 5.7% increase in O3 Heavy-duty truck emissions contribute primarily to these variations. Future traffic-emission controls are estimated to impose similar effects as observed during the COVID-19 lockdown, but with smaller magnitude. Vehicular electrification will achieve further alleviation of NO2 levels.

Societal shifts due to COVID-19 reveal large-scale complexities and feedbacks between atmospheric chemistry and climate change.

The COVID-19 global pandemic and associated government lockdowns dramatically altered human activity, providing a window into how changes in individual behavior, enacted en masse, impact atmospheric composition. The resulting reductions in anthropogenic activity represent an unprecedented event that yields a glimpse into a future where emissions to the atmosphere are reduced. Furthermore, the abrupt reduction in emissions during the lockdown periods led to clearly observable changes in atmospheric composition, which provide direct insight into feedbacks between the Earth system and human activity. While air pollutants and greenhouse gases share many common anthropogenic sources, there is a sharp difference in the response of their atmospheric concentrations to COVID-19 emissions changes, due in large part to their different lifetimes. Here, we discuss several key takeaways from modeling and observational studies. First, despite dramatic declines in mobility and associated vehicular emissions, the atmospheric growth rates of greenhouse gases were not slowed, in part due to decreased ocean uptake of CO2 and a likely increase in CH4 lifetime from reduced NO x emissions. Second, the response of O3 to decreased NO x emissions showed significant spatial and temporal variability, due to differing chemical regimes around the world. Finally, the overall response of atmospheric composition to emissions changes is heavily modulated by factors including carbon-cycle feedbacks to CH4 and CO2, background pollutant levels, the timing and location of emissions changes, and climate feedbacks on air quality, such as wildfires and the ozone climate penalty.

SPINK2 Protein Expression Is an Independent Adverse Prognostic Marker in AML and Is Potentially Implicated in the Regulation of Ferroptosis and Immune Response.

There is an urgent need for the identification as well as clinicopathological and functional characterization of potent prognostic biomarkers and therapeutic targets in acute myeloid leukemia (AML). Using immunohistochemistry and next-generation sequencing, we investigated the protein expression as well as clinicopathological and prognostic associations of serine protease inhibitor Kazal type 2 (SPINK2) in AML and examined its potential biological functions. High SPINK2 protein expression was an independent adverse biomarker for survival and an indicator of elevated therapy resistance and relapse risk. SPINK2 expression was associated with AML with an NPM1 mutation and an intermediate risk by cytogenetics and European LeukemiaNet (ELN) 2022 criteria. Furthermore, SPINK2 expression could refine the ELN2022prognostic stratification. Functionally, an RNA sequencing analysis uncovered a potential link of SPINK2 with ferroptosis and immune response. SPINK2 regulated the expression of certain P53 targets and ferroptosis-related genes, including SLC7A11 and STEAP3, and affected cystine uptake, intracellular iron levels and sensitivity to erastin, a specific ferroptosis inducer. Furthermore, SPINK2 inhibition consistently increased the expression of ALCAM, an immune response enhancer and promoter of T-cell activity. Additionally, we identified a potential small-molecule inhibitor of SPINK2, which requires further characterization. In summary, high SPINK2 protein expression was a potent adverse prognostic marker in AML and might represent a druggable target.

Quantifying Northern High Latitude Gross Primary Productivity (GPP) Using Carbonyl Sulfide (OCS).

The northern high latitude (NHL, 40°N to 90°N) is where the second peak region of gross primary productivity (GPP) other than the tropics. The summer NHL GPP is about 80% of the tropical peak, but both regions are still highly uncertain (Norton et al. 2019, https://doi.org/10.5194/bg-16-3069-2019). Carbonyl sulfide (OCS) provides an important proxy for photosynthetic carbon uptake. Here we optimize the OCS plant uptake fluxes across the NHL by fitting atmospheric concentration simulation with the GEOS-CHEM global transport model to the aircraft profiles acquired over Alaska during NASA's Carbon in Arctic Reservoirs Vulnerability Experiment (2012-2015). We use the empirical biome-specific linear relationship between OCS plant uptake flux and GPP to derive the six plant uptake OCS fluxes from different GPP data. Such GPP-based fluxes are used to drive the concentration simulations. We evaluate the simulations against the independent observations at two ground sites of Alaska. The optimized OCS fluxes suggest the NHL plant uptake OCS flux of -247 Gg S year-1, about 25% stronger than the ensemble mean of the six GPP-based OCS fluxes. GPP-based OCS fluxes systematically underestimate the peak growing season across the NHL, while a subset of models predict early start of season in Alaska, consistent with previous studies of net ecosystem exchange. The OCS optimized GPP of 34 PgC yr-1 for NHL is also about 25% more than the ensembles mean from six GPP data. Further work is needed to fully understand the environmental and biotic drivers and quantify their rate of photosynthetic carbon uptake in Arctic ecosystems.

Computation by Convective Logic Gates and Thermal Communication.

We demonstrate a novel computational architecture based on fluid convection logic gates and heat flux-mediated information flows. Our previous work demonstrated that Boolean logic operations can be performed by thermally driven convection flows. In this work, we use numerical simulations to demonstrate a different , but universal Boolean logic operation (NOR), performed by simpler convective gates. The gates in the present work do not rely on obstacle flows or periodic boundary conditions, a significant improvement in terms of experimental realizability. Conductive heat transfer links can be used to connect the convective gates, and we demonstrate this with the example of binary half addition. These simulated circuits could be constructed in an experimental setting with modern, 2-dimensional fluidics equipment, such as a thin layer of fluid between acrylic plates. The presented approach thus introduces a new realm of unconventional, thermal fluid-based computation.

ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses.

G proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze GTP. The YchF subfamily, interestingly, possesses the unique ability to bind both ATP and GTP, and is possibly an ancestral form of G proteins based on phylogenetic studies and is present in all kingdoms of life. However, the biological significance of such a relaxed ligand specificity has long eluded researchers. Here, we have elucidated the different conformational changes caused by the binding of a YchF homolog in rice (OsYchF1) to ATP versus GTP by X-ray crystallography. Furthermore, by comparing the 3D relationships of the ligand position and the various amino acid residues at the binding sites in the crystal structures of the apo-bound and ligand-bound versions, a mechanism for the protein's ability to bind both ligands is revealed. Mutation of the noncanonical G4 motif of the OsYchF1 to the canonical sequence for GTP specificity precludes the binding/hydrolysis of ATP and prevents OsYchF1 from functioning as a negative regulator of plant-defense responses, while retaining its ability to bind/hydrolyze GTP and its function as a negative regulator of abiotic stress responses, demonstrating the specific role of ATP-binding/hydrolysis in disease resistance. This discovery will have a significant impact on our understanding of the structure-function relationships of the YchF subfamily of G proteins in all kingdoms of life.

Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1).

The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that a member of this group, OsGAP1, is able to alleviate salt stress and stimulate defense responses, and bind to both phospholipids and an unconventional G-protein, OsYchF1. Here we solved the crystal structure of OsGAP1 to a resolution of 1.63 Å. Using site-directed mutagenesis, we successfully differentiated between the clusters of surface residues that are required for binding to phospholipids versus OsYchF1, which, in turn, is critical for its role in stimulating defense responses. On the other hand, the ability to alleviate salt stress by OsGAP1 is dependent only on its ability to bind OsYchF1 and is independent of its phospholipid-binding activity.

Midlatitude atmospheric OH response to the most recent 11-y solar cycle.

The hydroxyl radical (OH) plays an important role in middle atmospheric photochemistry, particularly in ozone (O(3)) chemistry. Because it is mainly produced through photolysis and has a short chemical lifetime, OH is expected to show rapid responses to solar forcing [e.g., the 11-y solar cycle (SC)], resulting in variabilities in related middle atmospheric O(3) chemistry. Here, we present an effort to investigate such OH variability using long-term observations (from space and the surface) and model simulations. Ground-based measurements and data from the Microwave Limb Sounder on the National Aeronautics and Space Administration's Aura satellite suggest an ∼7-10% decrease in OH column abundance from solar maximum to solar minimum that is highly correlated with changes in total solar irradiance, solar Mg-II index, and Lyman-α index during SC 23. However, model simulations using a commonly accepted solar UV variability parameterization give much smaller OH variability (∼3%). Although this discrepancy could result partially from the limitations in our current understanding of middle atmospheric chemistry, recently published solar spectral irradiance data from the Solar Radiation and Climate Experiment suggest a solar UV variability that is much larger than previously believed. With a solar forcing derived from the Solar Radiation and Climate Experiment data, modeled OH variability (∼6-7%) agrees much better with observations. Model simulations reveal the detailed chemical mechanisms, suggesting that such OH variability and the corresponding catalytic chemistry may dominate the O(3) SC signal in the upper stratosphere. Continuing measurements through SC 24 are required to understand this OH variability and its impacts on O(3) further.

New Estimates of Nitrogen Fixation on Early Earth.

Fixed nitrogen species generated by the early Earth's atmosphere are thought to be critical to the emergence of life and the sustenance of early metabolisms. A previous study estimated nitrogen fixation in the Hadean Earth's N2/CO2-dominated atmosphere; however, that previous study only considered a limited chemical network that produces NOx species (i.e., no HCN formation) via the thermochemical dissociation of N2 and CO2 in lightning flashes, followed by photochemistry. Here, we present an updated model of nitrogen fixation on Hadean Earth. We use the Chemical Equilibrium with Applications (CEA) thermochemical model to estimate lightning-induced NO and HCN formation and an updated version of KINETICS, the 1-D Caltech/JPL photochemical model, to assess the photochemical production of fixed nitrogen species that rain out into the Earth's early ocean. Our updated photochemical model contains hydrocarbon and nitrile chemistry, and we use a Geant4 simulation platform to consider nitrogen fixation stimulated by solar energetic particle deposition throughout the atmosphere. We study the impact of a novel reaction pathway for generating HCN via HCN2, inspired by the experimental results which suggest that reactions with CH radicals (from CH4 photolysis) may facilitate the incorporation of N into the molecular structure of aerosols. When the HCN2 reactions are added, we find that the HCN rainout rate rises by a factor of five in our 1-bar case and is about the same in our 2- and 12-bar cases. Finally, we estimate the equilibrium concentration of fixed nitrogen species under a kinetic steady state in the Hadean ocean, considering loss by hydrothermal vent circulation, photoreduction, and hydrolysis. These results inform our understanding of environments that may have been relevant to the formation of life on Earth, as well as processes that could lead to the emergence of life elsewhere in the universe.

The unconventional P-loop NTPase OsYchF1 and its regulator OsGAP1 play opposite roles in salinity stress tolerance.

YchF proteins are a group of mysterious but ubiquitous unconventional G-proteins found in all kingdoms of life except Archaea. Their functions have been documented in microorganisms, protozoa and human, but those of plant YchF homologues are largely unknown. Our group has previously shown that OsYchF1 and its interacting protein, OsGAP1, play opposite roles in plant defense responses. OsGAP1 was found to stimulate the GTPase/ATPase activities of OsYchF1 and regulate its subcellular localization. In this report, we demonstrate that both OsYchF1 and OsGAP1 are localized mainly in the cytosol under NaCl treatment. The ectopic expression of OsYchF1 in transgenic Arabidopsis thaliana leads to reduced tolerance towards salinity stress, while the ectopic expression of OsGAP1 has the opposite effect. Similar results were also obtained with the Arabidopsis homologues, AtYchF1 and AtGAP1, by using AtGAP1 overexpressors and underexpressors, as well as an AtYchF1-knockdown mutant. OsYchF1 and OsGAP1 also exhibit highly significant effects on salinity-induced oxidative stress tolerance. The expression of OsYchF1 suppresses the anti-oxidation enzymatic activities and increases lipid peroxidation in transgenic Arabidopsis, and leads to the accumulation of reactive oxygen species (ROS) in tobacco BY-2 cells, while the ectopic expression of OsGAP1 has the opposite effects in these two model systems.

Water vapour in the atmosphere of a transiting extrasolar planet.

Water is predicted to be among the most abundant (if not the most abundant) molecular species after hydrogen in the atmospheres of close-in extrasolar giant planets ('hot Jupiters'). Several attempts have been made to detect water on such planets, but have either failed to find compelling evidence for it or led to claims that should be taken with caution. Here we report an analysis of recent observations of the hot Jupiter HD 189733b (ref. 6) taken during the transit, when the planet passed in front of its parent star. We find that absorption by water vapour is the most likely cause of the wavelength-dependent variations in the effective radius of the planet at the infrared wavelengths 3.6 mum, 5.8 mum (both ref. 7) and 8 mum (ref. 8). The larger effective radius observed at visible wavelengths may arise from either stellar variability or the presence of clouds/hazes. We explain the report of a non-detection of water on HD 189733b (ref. 4) as being a consequence of the nearly isothermal vertical profile of the planet's atmosphere.

Tropical mid-tropospheric CO2 variability driven by the Madden-Julian oscillation.

Carbon dioxide (CO(2)) is the most important anthropogenic greenhouse gas in the present-day climate. Most of the community focuses on its long-term (decadal to centennial) behaviors that are relevant to climate change, but there are relatively few discussions of its higher-frequency forms of variability, and none regarding its subseasonal distribution. In this work, we report a large-scale intraseasonal variation in the Atmospheric Infrared Sounder CO(2) data in the global tropical region associated with the Madden-Julian oscillation (MJO). The peak-to-peak amplitude of the composite MJO modulation is ∼1 ppmv, with a standard error of the composite mean < 0.1 ppmv. The correlation structure between CO(2) and rainfall and vertical velocity indicate positive (negative) anomalies in CO(2) arise due to upward (downward) large-scale vertical motions in the lower troposphere associated with the MJO. These findings can help elucidate how faster processes can organize, transport, and mix CO(2) and provide a robustness test for coupled carbon-climate models.

Decadal decrease in Los Angeles methane emissions is much smaller than bottom-up estimates.

Methane, a powerful greenhouse gas, has a short atmospheric lifetime ( ~ 12 years), so that emissions reductions will have a rapid impact on climate forcing. In megacities such as Los Angeles (LA), natural gas (NG) leakage is the primary atmospheric methane source. The magnitudes and trends of fugitive NG emissions are largely unknown and need to be quantified to verify compliance with emission reduction targets. Here we use atmospheric remote sensing data to show that, in contrast to the observed global increase in methane emissions, LA area emissions decreased during 2011-2020 at a mean rate of (-1.57 ± 0.41) %/yr. However, the NG utility calculations indicate a much larger negative emissions trend of -5.8 %/yr. The large difference between top-down and bottom-up trends reflects the uncertainties in estimating the achieved emissions reductions. Actions taken in LA can be a blueprint for COP28 and future efforts to reduce methane emissions.

Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia.

Pediatric acute myeloid leukemia (AML) is an uncommon but aggressive hematological malignancy. The poor outcome is attributed to inadequate prognostic classification and limited treatment options. A thorough understanding on the genetic basis of pediatric AML is important for the development of effective approaches to improve outcomes. Here, by comprehensively profiling fusion genes as well as mutations and copy number changes of 141 myeloid-related genes in 147 pediatric AML patients with subsequent variant functional characterization, we unveil complex mutational patterns of biological relevance and disease mechanisms including MYC deregulation. Also, our findings highlight TP53 alterations as strong adverse prognostic markers in pediatric AML and suggest the core spindle checkpoint kinase BUB1B as a selective dependency in this aggressive subgroup. Collectively, our present study provides detailed genomic characterization revealing not only complexities and mechanistic insights into pediatric AML but also significant risk stratification and therapeutic strategies to tackle the disease.

Atmospheric pressure as a natural climate regulator for a terrestrial planet with a biosphere.

Lovelock and Whitfield suggested in 1982 that, as the luminosity of the Sun increases over its life cycle, biologically enhanced silicate weathering is able to reduce the concentration of atmospheric carbon dioxide (CO(2)) so that the Earth's surface temperature is maintained within an inhabitable range. As this process continues, however, between 100 and 900 million years (Ma) from now the CO(2) concentration will reach levels too low for C(3) and C(4) photosynthesis, signaling the end of the solar-powered biosphere. Here, we show that atmospheric pressure is another factor that adjusts the global temperature by broadening infrared absorption lines of greenhouse gases. A simple model including the reduction of atmospheric pressure suggests that the life span of the biosphere can be extended at least 2.3 Ga into the future, more than doubling previous estimates. This has important implications for seeking extraterrestrial life in the Universe. Space observations in the infrared region could test the hypothesis that atmospheric pressure regulates the surface temperature on extrasolar planets.

Evaluation of Modeled Hyperspectral Infrared Spectra Against All-Sky AIRS Observations Using Different Cloud Overlap Schemes.

Hyperspectral infrared sounding contains information about clouds, which plays an important role in modulating Earth's climate. However, there is a great deal of uncertainty in modeling the radiative effect of clouds due to its complex dependence on various parameters. Therefore, cloudy scenarios are often neglected in retrievals of infrared spectral measurements and in data assimilation. One-dimensional radiative transfer (RT) models have a limited capability to represent the cloud three-dimensional multilayer structure. This issue is typically resolved by using a multiple independent column approach, which is computationally demanding. Therefore, it is necessary to find a balance between computational speed and accuracy for infrared RT all-sky radiance simulations. In this study, we utilize the Community Radiative Transfer Model with four different cloud overlap schemes and compare against observations made by the Atmospheric Infrared Sounder (AIRS) using a statistical metric called the first Wasserstein distance. Our results show that the average cloud overlap scheme performs the best and successfully predicts the overall probability distribution of brightness temperature over nonfrozen oceans for a wide range of wavelengths. The mean absolute differences are less than 0.7 K for 846 selected AIRS channels between 790 cm-1 and 1231 cm-1.

Seasonal Variations of Solar-Induced Fluorescence, Precipitation, and Carbon Dioxide Over the Amazon.

Previous studies suggested that the Amazon, the largest rainforest on Earth, changes from a CO2 sink to a CO2 source during the dry/fire season. However, the biospheric contributions to atmospheric CO2 are not well understood during the two main seasons, the dry/fire season and the wet season. In this article, we utilize Orbiting Carbon Observatory 2 (OCO-2) Solar-Induced Fluorescence (SIF) to explore photosynthetic activity during the different seasons. The spatiotemporal variability of OCO-2 SIF, OCO-2 CO2, precipitation, and burned area are investigated over the Amazon from September 2014 to December 2019. Averaging over the entire Amazon region, we found a positive temporal correlation (0.94) between OCO-2 SIF and Global Precipitation Climatology Project precipitation and a negative temporal correlation (-0.64) between OCO-2 SIF and OCO-2 CO2, consistent with the fact that precipitation enhances photosynthesis, which results in higher values for SIF and rate of removal of CO2 from the atmosphere above the Amazon region. We also observed seasonality in the spatial variability of these variables within the Amazon region. During the dry/fire (August-October) season, low SIF values, low precipitation, high vapor pressure deficit (VPD), large burned areas, and high atmospheric CO2 are mainly found over the southern Amazon region. In contrast, during the wet season (January-March), high SIF values, high precipitation, low VPD, smaller burned areas, and low CO2 are found over both the central and southern Amazon regions. The seasonal difference in SIF suggests that photosynthetic activity is reduced during the dry/fire season relative to the wet season as a result of low precipitation and high VPD, especially over the southern Amazon region, which will contribute to more CO2 in the atmosphere during the dry/fire season.

A bimodal distribution of haze in Pluto's atmosphere.

Pluto, Titan, and Triton make up a unique class of solar system bodies, with icy surfaces and chemically reducing atmospheres rich in organic photochemistry and haze formation. Hazes play important roles in these atmospheres, with physical and chemical processes highly dependent on particle sizes, but the haze size distribution in reducing atmospheres is currently poorly understood. Here we report observational evidence that Pluto's haze particles are bimodally distributed, which successfully reproduces the full phase scattering observations from New Horizons. Combined with previous simulations of Titan's haze, this result suggests that haze particles in reducing atmospheres undergo rapid shape change near pressure levels ~0.5 Pa and favors a photochemical rather than a dynamical origin for the formation of Titan's detached haze. It also demonstrates that both oxidizing and reducing atmospheres can produce multi-modal hazes, and encourages reanalysis of observations of hazes on Titan and Triton.

A novel NUP98-JADE2 fusion in a patient with acute myeloid leukemia resembling acute promyelocytic leukemia.

Acute promyelocytic leukemia (APL) is a specific subtype of acute myeloid leukemia (AML) characterized by block of differentiation at the promyelocytic stage and the presence of PML-RARA fusion. In rare instances, RARA is fused with other partners in variant APL. More infrequently, non-RARA genes are rearranged in AML patients resembling APL. However, the underlying disease pathogenesis in these atypical cases is largely unknown. Here, we report the identification and characterization of a NUP98- JADE2 fusion in a pediatric AML patient showing APL-like morphology and immunophenotype. Mechanistically, we showed that NUP98-JADE2 could impair all-trans retinoic acid (ATRA)-mediated transcriptional control and myeloid differentiation. Intriguingly, NUP98-JADE2 was found to alter the subcellular distribution of wild-type JADE2, whose down-regulation similarly led to attenuated ATRA-induced responses and myeloid activation, suggesting that NUP98-JADE2 may mediate JADE2 inhibition. To our knowledge, this is the first report of a NUP98-non-RAR rearrangement identified in an AML patient mimicking APL. Our findings suggest JADE2 as a novel myeloid player involved in retinoic acid-induced differentiation. Despite lacking a rearranged RARA, our findings implicate that altered retinoic acid signaling by JADE2 disruption may underlie the APL-like features in our case, corroborating the importance of this signaling in APL pathogenesis.