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At least 595 records · Page 33

Fluorination Enables Simultaneous Improvements of a Dialkoxybenzene-Based Redoxmer for Nonaqueous Redox Flow Batteries

Redoxmers or redox-active organic materials, arc one critical component for nonaqueous redox flow batteries (RFBs), which hold high promise in enabling the time domain of the grid. While tuning redox potentials of redoxmers is a very effective way to enhance energy densities of NRFBs, those improvements often accompany accelerated kinetics of the charged species, undermining stability and cycling performance. In this paper, a strategy for designing redoxmers with simultaneous improvements in redox potential and stability is proposed. Specifically, the redoxmer 1,4-di-tert-butyl-2,5-bis(2,2,2-trifluoroethoxy)benzene (ANL-C46) is developed by incorporating fluorinated substitutions into the dialkoxybenzene-based platform. Compared to the non-fluorinated analogue, ANL-C46 demonstrates not only an increased (similar to 0.41 V) redox potential but also much enhanced stability (1.6 times) and cyclability (4 times) evidenced by electron paramagnetic resonance kinetic study, H-cell and flow cell cycling. In fact, the cycling performance of ANL-C46 is among the best of high potential (>1.0 V vs Ag/Ag + ) redoxmers ever reported. Density functional theory calculations suggest that while the introduced fluorine substitutions elevate the redox potentials, they also help to depress the decomposition reactions of the charged redoxmers, affording excellent stability. The findings represent an interesting strategy for simultaneously improving energy density and stability, which could further prompt the development of high-performance redoxmers.

25 ENERGY STORAGE↗

Release Factor Inhibiting Antimicrobial Peptides Improve Nonstandard Amino Acid Incorporation in Wild-type Bacterial Cells

We report a tunable chemical genetics approach for enhancing genetic code expansion in different wild-type bacterial strains that employs apidaecin-like, anti-microbial peptides observed to temporarily sequester and thereby inhibit Release Factor 1 (RF1). In a concentration-dependent matter, these peptides granted a conditional lambda phage resistance to a recoded Escherichia coli strain with non-essential RF1 activity and promoted multi-site non-standard amino acid (nsAA) incorporation at in-frame amber stop codons in vivo and in vitro. When exogenously added, the peptides stimulated specific nsAA incorporation in a variety of sensitive, wild-type (RF1+) strains including Agrobacterium tumefaciens, a species in which nsAA incorporation has not been previously reported. Improvement in nsAA incorporation was typically 2–15-fold in E. coli BL21, MG1655, DH10B strains and A. tumefaciens with the >20-fold improvement observed in probiotic E. coli Nissle 1917. In-cell expression of these peptides promoted multi-site nsAA incorporation in transcripts with up to 6 amber codons, with a >35-fold increase in BL21 showing moderate toxicity. Leveraging this RF1 sensitivity allowed multiplexed partial recoding of MG1655 and DH10B that rapidly resulted in resistant strains that showed an additional ~2 fold boost to nsAA incorporation independent of the peptide. Lastly, in-cell expression of an apidaecin-like peptide library allowed the discovery of new peptide variants with reduced toxicity that still improved multi-site nsAA incorporation >25-fold. In parallel to genetic reprogramming efforts, these new approaches can facilitate genetic code expansion technologies in a variety of wild-type bacterial strains.

59 BASIC BIOLOGICAL SCIENCES↗

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a non-model bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in non-model organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T 7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool’s utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. In conclusion, our CRISPRi tool will be useful to facilitate functional studies of this non-model organism and engineer this promising microbial chassis for lignin valorization.

09 BIOMASS FUELS↗

Parameterizing Subgrid Variations of Land Surface Heat Fluxes to the Atmosphere Improves Boreal Summer Land Precipitation Simulation With the NCAR CESM1.2

Subgrid horizontal variations of land surface heat fluxes to the atmosphere resulting from subgrid land cover heterogeneity are important in land-atmosphere interaction in global climate models (GCMs). To incorporate it, a parameterization using stochastic sampling based on truncated normal distributions diagnosed from the land model and internal ensemble mean of multiple calls to the planetary boundary layer and deep convection schemes is developed. After its implementation in the National Center for Atmospheric Research (NCAR) Community Earth System Model version 1.2 (CESM1.2), large changes of simulated land precipitation are found to occur in regions where large subgrid variations of surface heat fluxes exist. The simulated precipitation is improved in boreal summer, especially over eastern China and the coastal areas of the Bay of Bengal. The improved precipitation is mainly a result of improved large-scale moisture convergence and advection by altered vertical diffusion and convection.

58 GEOSCIENCES↗

Improved Convective Ice Microphysics Parameterization in the NCAR CAM Model

Partitioning deep convective cloud condensates into components that sediment and detrain, known to be a challenge for global climate models, is important for cloud vertical distribution and anvil cloud formation. In this study, we address this issue by improving the convective microphysics scheme in the National Center for Atmospheric Research Community Atmosphere Model version 5.3 (CAM5.3). The improvements include: (1) considering sedimentation for cloud ice crystals that do not fall in the original scheme, (2) applying a new terminal velocity parameterization that depends on the environmental conditions for convective snow, (3) adding a new hydrometeor category, “rimed ice,” to the original four-class (cloud liquid, cloud ice, rain, and snow) scheme, and (4) allowing convective clouds to detrain snow particles into stratiform clouds. Results from the default and modified CAM5.3 models were evaluated against observations from the U.S. Department of Energy Tropical Warm Pool-International Cloud Experiment (TWP-ICE) field campaign. The default model overestimates ice amount, which is largely attributed to the underestimation of convective ice particle sedimentation. By considering cloud ice sedimentation and rimed ice particles and applying a new convective snow terminal velocity parameterization, the vertical distribution of ice amount is much improved in the midtroposphere and upper troposphere when compared to observations. The vertical distribution of ice condensate also agrees well with observational best estimates upon considering snow detrainment. Further, comparison with observed convective updrafts reveals that current bulk model fails to reproduce the observed updraft magnitude and occurrence frequency, suggesting spectral distributions be required to simulate the subgrid updraft heterogeneity.

54 ENVIRONMENTAL SCIENCES↗

An Improved Representation of Aerosol Wet Removal by Deep Convection and Impacts on Simulated Aerosol Vertical Profiles

Here, we introduce a physics-based aerosol wet removal scheme with unified treatments of aerosol transport and removal by convective clouds into the Community Atmosphere Model version 6. Since several important physical processes are still neglected or poorly represented in this new physics-based scheme, we develop secondary improvements to the parameterizations of aerosol activation, resuspension, and cloud-borne aerosol detrainment in this new scheme. Changes in the aerosol wet removal scheme cause tropospheric aerosol concentrations to decrease to different extents: compared to the control run, the physics-based scheme significantly decreases aerosol burdens by up to 60% over the southern Pacific Ocean, whereas the secondary improvements mitigate the decreasing tendency. The burden changes also depend on aerosol chemical components: the sulfate mass decrease is compensated by secondary production, black carbon (BC) is effectively removed via increasing the hygroscopicity of particulate organic matter from 0 to 0.2, and dust shows the most spatially heterogeneous changes. Simulated aerosol profiles are evaluated against aircraft-based observations over the Pacific and Atlantic Oceans. The secondary-improved scheme reduces the overestimations of upper tropospheric BC and sea salt concentrations by a factor of 10 and 1,000, respectively, and reproduces the dependence of BC mass decrease rates on cloud types. Consideration of convective cloud-borne aerosol detrainment plays the most important role in enhancing the aerosol wet removal and decreasing the positive biases of tropospheric BC and sea salt concentrations. We also summarize unresolved issues related to convective cloud genesis and microphysics, cloud-borne aerosol evolution, and BC and dust emissions.

54 ENVIRONMENTAL SCIENCES↗

Ensemble‐Based Assimilation of Satellite All‐Sky Microwave Radiances Improves Intensity and Rainfall Predictions for Hurricane Harvey (2017)

Abstract Ensemble‐based data assimilation of radar observations across inner‐core regions of tropical cyclones (TCs) in tandem with satellite all‐sky infrared (IR) radiances across the TC domain improves TC track and intensity forecasts. This study further investigates potential enhancements in TC track, intensity, and rainfall forecasts via assimilation of all‐sky microwave (MW) radiances using Hurricane Harvey (2017) as an example. Assimilating Global Precipitation Measurement constellation all‐sky MW radiances in addition to GOES‐16 all‐sky IR radiances reduces the forecast errors in the TC track, rapid intensification (RI), and peak intensity compared to assimilating all‐sky IR radiances alone, including a 24‐hr increase in forecast lead‐time for RI. Assimilating all‐sky MW radiances also improves Harvey's hydrometeor fields, which leads to improved forecasts of rainfall after Harvey's landfall. This study indicates that avenues exist for producing more accurate forecasts for TCs using available yet underutilized data, leading to better warnings of and preparedness for TC‐associated hazards in the future.

54 ENVIRONMENTAL SCIENCES↗

WUS256: An Adjoint Waveform Tomography Model of the Crust and Upper Mantle of the Western United States for Improved Waveform Simulations

Abstract We report a new model (WUS256) of radially anisotropic seismic wavespeeds of the crust and upper mantle of the western United States (WUS) obtained from adjoint waveform tomography for the purpose of improving synthetic waveform fits to observed data. WUS256 is based on inversion of over 94,000 waveforms from 72 earthquakes recorded by nearly 3,400 stations. We started with the SPiRaL global model (Simmons et al., 2021, https://doi.org/10.1093/gji/ggab277 ) and waveforms in the period band of 50–120 s. We followed a conservative multiscale inversion approach with eight stages and 256 total inversion iterations which enabled monotonic misfit reduction to 20‐s minimum‐period waves. WUS256 relied on time‐frequency (TF) phase misfits and a trust region limited memory Broyden–Fletcher–Goldfarb–Shanno (L‐BFGS) optimization. Hessian‐vector products were used to qualitatively assess model resolution. Results indicate that WUS256 has good coverage of the continental regions to depths of about 150 km and is able to resolve features on lateral scales of about 200 km. We quantify waveform fits by the reduction in TF and normalized amplitude difference misfits between WUS256 and the SPiRaL starting model. WUS256 significantly improves waveform fits with misfit reduction 64% for both inversion and validation data sets compared to the SPiRaL starting model and shows even better fits compared to other models. Waveform fits illustrate that WUS256 reproduces body‐waves, fundamental mode surface waves as well as late arriving dispersed and/or scattered short period surface waves. The improvement in waveform fit indicates that WUS256 can be used to reproduce path effects on regional complete waveforms and moment tensor inversions.

58 GEOSCIENCES↗

Improving E3SM Land Model Photosynthesis Parameterization via Satellite SIF, Machine Learning, and Surrogate Modeling

The parameterization of key photosynthesis parameters is one of the key uncertain sources in modeling ecosystem gross primary productivity (GPP). Solar-induced chlorophyll fluorescence (SIF) offers a good proxy for GPP since it marks the actual process of photosynthesis; while machine learning (ML) provides a robust approach to model the GPP-SIF relationship. Here, we trained the boosted regressing tree (BRT) and the Random Forest ML models with Greenhouse Gases Observing Satellite SIF data and in situ GPP observations from 49 eddy covariance towers. These trained ML GPP-SIF models were fed into the Energy Exascale Earth System Model (E3SM) Land Model (ELM) to generate ELM-simulated global SIF estimates, which were then benchmarked against satellite SIF observations with a surrogate modeling approach. Our results indicated good modeling performance of the ML-based GPP-SIF relationship. The ELM model when fed with the ML GPP-SIF models also can well predict the spatial-temporal variations in SIF. We also found high model accuracy for the surrogate modeling. Model parameter sensitivity analysis suggested that the fraction of leaf nitrogen in RuBisCO (flnr) is the most sensitive parameter to the SIF; other sensitive parameters include the Ball-Berry stomatal conductance slope (mbbopt) and the vcmax entropy (vcmaxse). The posterior uncertainty in simulated GPP was greatly reduced after benchmarking, and the model produced improved spatial patterns of mean GPP relative to FLUXCOM GPP. Our integrated approach provides a new avenue for improving land models and using remote-sensing SIF, which can be further improved in the future with more ground- and satellite-based observations.

54 ENVIRONMENTAL SCIENCES↗

Toward Improved Regional Hydrological Model Performance Using State-Of-The-Science Data-Informed Soil Parameters

Accurate soil moisture and streamflow data are an aspirational need of many hydrologically relevant fields. Model simulated soil moisture and streamflow hold promise but models require validation prior to application. Calibration methods are commonly used to improve model fidelity but misrepresentation of the true dynamics remains a challenge. In this study, we leverage soil parameter estimates from the Soil Survey Geographic (SSURGO) database and the probability mapping of SSURGO (POLARIS) to improve the representation of hydrologic processes in the Weather Research and Forecasting Hydrological modeling system (WRF-Hydro) over a central California domain. Our results show WRF-Hydro soil moisture exhibits increased correlation coefficients ( r ), reduced biases, and increased Kling-Gupta Efficiencies (KGEs) across seven in situ soil moisture observing stations after updating the model's soil parameters according to POLARIS. Compared to four well-established soil moisture data sets including Soil Moisture Active Passive data and three Phase 2 North American Land Data Assimilation System land surface models, our POLARIS-adjusted WRF-Hydro simulations produce the highest mean KGE (0.69) across the seven stations. More importantly, WRF-Hydro streamflow fidelity also increases, especially in the case where the model domain is set up with SSURGO-informed total soil thickness. The magnitude and timing of peak flow events are better captured, r increases across nine United States Geological Survey stream gages, and the mean KGE across seven of the nine gages increases from 0.12 to 0.66. Our pre-calibration parameter estimate approach, which is transferable to other spatially distributed hydrological models, can substantially improve a model's performance, helping reduce calibration efforts and computational costs.

54 ENVIRONMENTAL SCIENCES↗

Improving River Routing Using a Differentiable Muskingum‐Cunge Model and Physics‐Informed Machine Learning

Recently, rainfall-runoff simulations in small headwater basins have been improved by methodological advances such as deep neural networks (NNs) and hybrid physics-NN models—particularly, a genre called differentiable modeling that intermingles NNs with physics to learn relationships between variables. However, hydrologic routing simulations, necessary for simulating floods in stem rivers downstream of large heterogeneous basins, had not yet benefited from these advances and it was unclear if the routing process could be improved via coupled NNs. We present a novel differentiable routing method (δMC-Juniata-hydroDL2) that mimics the classical Muskingum-Cunge routing model over a river network but embeds an NN to infer parameterizations for Manning's roughness (n) and channel geometries from raw reach-scale attributes like catchment areas and sinuosity. The NN was trained solely on downstream hydrographs. Synthetic experiments show that while the channel geometry parameter was unidentifiable, n can be identified with moderate precision. With real-world data, the trained differentiable routing model produced more accurate long-term routing results for both the training gage and untrained inner gages for larger subbasins (>2,000 km2) than either a machine learning model assuming homogeneity, or simply using the sum of runoff from subbasins. The n parameterization trained on short periods gave high performance in other periods, despite significant errors in runoff inputs. The learned n pattern was consistent with literature expectations, demonstrating the framework's potential for knowledge discovery, but the absolute values can vary depending on training periods. The trained n parameterization can be coupled with traditional models to improve national-scale hydrologic flood simulations.

54 ENVIRONMENTAL SCIENCES↗

Explicit Consideration of Plant Xylem Hydraulic Transport Improves the Simulation of Crop Response to Atmospheric Dryness in the U.S. Corn Belt

Abstract Atmospheric dryness (i.e., high vapor pressure deficit, VPD), together with soil moisture stress, limits plant photosynthesis and threatens ecosystem functioning. Regions where rainfall and soil moisture are relatively sufficient, such as the rainfed part of the U.S. Corn Belt, are especially prone to high VPD stress. With globally projected rising VPD under climate change, it is crucial to understand, simulate, and manage its negative impacts on agricultural ecosystems. However, most existing models simulating crop response to VPD are highly empirical and insufficient in capturing plant response to high VPD, and improved modeling approaches are urgently required. In this study, by leveraging recent advances in plant hydraulic theory, we demonstrate that the VPD constraints in the widely used coupled photosynthesis‐stomatal conductance models alone are inadequate to fully capture VPD stress effects. Incorporating plant xylem hydraulic transport significantly improves the simulation of transpiration under high VPD, even when soil moisture is sufficient. Our results indicate that the limited water transport capability from the plant root to the leaf stoma could be a major mechanism of plant response to high VPD stress. We then introduce a Demand‐side Hydraulic Limitation Factor (DHLF) that simplifies the xylem and the leaf segments of the plant hydraulic model to only one parameter yet captures the effect of plant hydraulic transport on transpiration response to high VPD with similar accuracy. We expect the improved understanding and modeling of crop response to high VPD to help contribute to better management and adaptation of agricultural systems in a changing climate.

Environmental Sciences & Ecology↗

Machine Learning Classification Strategy to Improve Streamflow Estimates in Diverse River Basins in the Colorado River Basin

Streamflow in the Colorado River Basin (CRB) is significantly altered by human activities including land use/cover alterations, reservoir operation, irrigation, and water exports. Climate is also highly varied across the CRB which contains snowpack-dominated watersheds and arid, precipitation-dominated basins. Recently, machine learning methods have improved the generalizability and accuracy of streamflow models. Previous successes with LSTM modeling have primarily focused on unimpacted basins, and few studies have included human impacted systems in either regional or single-basin modeling. We demonstrate that the diverse hydrological behavior of river basins in the CRB are too difficult to model with a single, regional model. We propose a method to delineate catchments into categories based on the level of predictability, hydrological characteristics, and the level of human influence. Lastly, we model streamflow in each category with climate and anthropogenic proxy data sets and use feature importance methods to assess whether model performance improves with additional relevant data. Overall, land use cover data at a low temporal resolution was not sufficient to capture the irregular patterns of reservoir releases, demonstrating the importance of having high-resolution reservoir release data sets at a global scale. On the other hand, the classification approach reduced the complexity of the data and has the potential to improve streamflow forecasts in human-altered regions.

54 ENVIRONMENTAL SCIENCES↗

Binary vector copy number engineering improves Agrobacterium -mediated transformation

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60–100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

Improvement of cryo-EM maps by density modification

A density-modification procedure for improving maps from single-particle electron cryogenic microscopy (cryo-EM) is presented here. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in cryo-EM, and that half-maps with independent errors are available in cryo-EM. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density-modification process. The density-modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.

47 OTHER INSTRUMENTATION↗

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗

Improvement of eukaryotic protein predictions from soil metagenomes

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

54 ENVIRONMENTAL SCIENCES↗

Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus

Developing an efficient deconstruction step of woody biomass for biorefinery has been drawing considerable attention since its xylem cell walls display highly recalcitrance nature. Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve saccharification efficiency in Populus species. First, 33 TF genes up-regulated during poplar wood formation were selected as potential regulators of xylem cell wall structure. The transgenic hybrid aspens (Populus tremula × Populus tremuloides) overexpressing each selected TF gene were screened for in vitro enzymatic saccharification. Of these, four transgenic seedlings overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average compared to control. The best performing lines overexpressing Pt × tERF123 and Pt × tZHD14 were further grown to form mature xylem in the greenhouse. Notably, the xylem cell walls exhibited significantly increased total xylan hydrolysis as well as initial hydrolysis rates of glucan. The increased saccharification of Pt × tERF123-overexpressing lines could reflect the improved balance of cell wall components, i.e., high cellulose and low xylan and lignin content, which could be caused by upregulation of cellulose synthase genes upon the expression of Pt × tERF123. Overall, we successfully identified Pt × tERF123 and Pt × tZHD14 as effective targets for reducing cell wall recalcitrance and improving the enzymatic degradation of woody plant biomass.

09 BIOMASS FUELS↗