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DOE OSTI2024

Machine learning enables identification of an alternative yeast galactose utilization pathway

How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype–phenotype map, and their application will uncover novel biology, even in well-studied traits.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2010

Terrestrial Hydrological Data from NASA's Hydrology Data and Information Services Center (HDISC): Products, Services, and Applications

Terrestrial hydrological variables are important in global hydrology, climate, and carbon cycle studies. The North American and Global Land Data Assimilation Systems (NLDAS and GLDAS, respectively) have been generating a series of land surface states (soil moisture, snow, and temperature) and fluxes (evapotranspiration, radiation, and heat flux) variables. These data, hosted at and available from NASA s Hydrology Data and Information Services Center (HDISC), include the NLDAS hourly 1/8 degree products and the GLDAS 3-hourly 0.25 and 1.0 degree products. HDISC provides easy access and visualization and analysis capabilities for these products, thus reducing the time and resources spent by scientists on data management and facilitating hydrological research. Users can perform spatial and parameter subsetting, data format transformation, and data analysis operations without needing to first download the data. HDISC is continually being developed as a data and services portal that supports weather and climate forecasts, and water and energy cycle research.

Fang, Hongliang↗

NASA NTRS2020

Observing System Simulation Experiments Investigating Atmospheric Motion Vectors and Radiances from a Constellation of 4-5 μm Infrared Sounders

A set of Observing System Simulation Experiments (OSSEs) was performed to investigate the utility of a constellation of passive infrared spectrometers, strategically designed with the aim of deriving the three-dimensional retrievals of the horizontal wind via atmospheric motion vectors (AMVs) from instruments with the spectral resolution of an infrared sounder. The instrument and constellation designs were performed in the context of the Midwave Infrared Sounding of Temperature and humidity in a Constellation for Winds, or MISTiC Winds. The Global Modeling and Assimilation Office OSSE system, which includes a full suite of operational meteorological observations, served as the control. To illustrate the potential impact of this observing strategy, two experiments were performed by adding the new simulated observations to the control. First, perfect (error-free) simulated AMVs and radiances were assimilated. Second, the data were made imperfect by adding realistic modeled errors to the AMVs and radiances that were assimilated. The experimentation showed beneficial impacts on both the mass and wind fields, as based on analysis verification, forecast verification, and the assessment of the observations using the Forecast Sensitivity to Observation Impact (FSOI) metric. In all variables and metrics, the impacts of the imperfect observations were smaller than those of the perfect observations, though much of the positive benefit was retained. The FSOI metric illustrated two key points. First, the largest impacts were seen in the middle troposphere AMVs, which is a targeted capability of the constellation strategy. Second, the addition of modeled errors showed that the assimilation system was unable to fully exploit the 4.3 μm carbon dioxide absorption radiances.

Will McCarty↗

NASA NTRS2021

Observing System Simulation Experiments Investigating Atmospheric Motion Vectors and Radiances from a Constellation of 4–5-μm Infrared Sounders

A set of observing system simulation experiments (OSSEs) was performed to investigate the utility of a constellation of passive infrared spectrometers, strategically designed with the aim of deriving the three-dimensional retrievals of the horizontal wind via atmospheric motion vectors (AMVs) from instruments with the spectral resolution of an infrared sounder. The instrument and constellation designs were performed in the context of the Midwave Infrared Sounding of Temperature and humidity in a Constellation for Winds (MISTiC Winds). The Global Modeling and Assimilation Office OSSE system, which includes a full suite of operational meteorological observations, served as the control. To illustrate the potential impact of this observing strategy, two experiments were performed by adding the new simulated observations to the control. First, perfect (error free) simulated AMVs and radiances were assimilated. Second, the data were made imperfect by adding realistic modeled errors to the AMVs and radiances that were assimilated. The experimentation showed beneficial impacts on both the mass and wind fields, as based on analysis verification, forecast verification, and the assessment of the observations using the forecast sensitivity to observation impact (FSOI) metric. In all variables and metrics, the impacts of the imperfect observations were smaller than those of the perfect observations, although much of the positive benefit was retained. The FSOI metric illustrated two key points. First, the largest impacts were seen in the middle troposphere AMVs, which is a targeted capability of the constellation strategy. Second, the addition of modeled errors showed that the assimilation system was unable to fully exploit the 4.3-μm carbon dioxide absorption radiances.

Will McCarty↗

DOE OSTI2022

The intermediate in a nitrate-responsive ω-amidase pathway in plants may signal ammonium assimilation status

Abstract A metabolite of ammonium assimilation was previously theorized to be involved in the coordination of the overall nitrate response in plants. Here we show that 2-hydroxy-5-oxoproline, made by transamination of glutamine, the first product of ammonium assimilation, may be involved in signaling a plant’s ammonium assimilation status. In leaves, 2-hydroxy-5-oxoproline met four foundational requirements to be such a signal. First, when it was applied to foliage, enzyme activities of nitrate reduction and ammonium assimilation increased; the activities of key tricarboxylic acid cycle-associated enzymes that help to supply carbon skeletons for amino acid synthesis also increased. Second, its leaf pools increased as nitrate availability increased. Third, the pool size of its precursor, Gln, reflected ammonium assimilation rather than photorespiration. Fourth, it was widely conserved among monocots, dicots, legumes, and nonlegumes and in plants with C3 or C4 metabolism. Made directly from the first product of ammonium assimilation, 2-hydroxy-5-oxoproline acted as a nitrate uptake stimulant. When 2-hydroxy-5-oxoproline was provided to roots, the plant’s nitrate uptake rate approximately doubled. Plants exogenously provided with 2-hydroxy-5-oxoproline to either roots or leaves accumulated greater biomass. A model was constructed that included the proposed roles of 2-hydroxy-5-oxoproline as a signal molecule of ammonium assimilation status in leaves, as a stimulator of nitrate uptake by roots and nitrate downloading from the xylem. In summary, a glutamine metabolite made in the ω-amidase pathway stimulated nitrate uptake by roots and was likely to be a signal of ammonium assimilation status in leaves. A chemical synthesis method for 2-hydroxy-5-oxoproline was also developed.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1991

Paleobiomarkers and defining exobiology experiments for future Mars experiments

Mars is a cold, dry planet with an oxidizing surface bombarded by ultraviolet and ionizing radiation, making prospects for an extant Mars biota bleak. Yet, it is suggested that early Earth and early Mars were similar enought that life may have evoled on Mars. If life did evolve on Mars, what evidence for its existence might we find? What constitutes a Martian paleobiomarker, and how can we distinguish such a marker from abiotically produced substances? The topics studied to answer this question include carbon and nitrogen cycling, as well as the stability and relative abundance of their intermediates in microbially dominated ecosystems. The microbially dominated ecosystems studied are the crytoendolithic microbial community living within sand rocks, the endoevaporite microbial community living inside salt crystals, and the microbial communities living beneath perennially ice-covered lakes and hypersaline ponds. The nitrogen cycle of these communities ranges from simple, where only assimilation occurs, to the more complex, where a complete cycle occurs. The carbon cycle of these communities appears to be complete.

Mancinelli, R. L.↗

NASA NTRS2019

Near Real-Time Global Composition Forecasts at 25km Horizontal Resolution

We present a new high-resolution global composition forecast system produced by NASA's Global Modeling and Assimilation Office. The NASA Goddard Earth Observing System (GEOS) model has been expanded to provide global near-real-time 5-day forecasts of atmospheric composition at unprecedented horizontal resolution of 0.25 degrees (~25 km). This composition forecast system (GEOS-CF) system combines the operational GEOS weather forecasting model with the state-of-the-science GEOS-Chem chemistry module (version 12) to provide detailed analysis of a wide range of air pollutants such as ozone, carbon monoxide, nitrogen oxides, and fine particulate matter (PM2.5). Satellite observations are assimilated into the system for improved representation of weather and smoke.

Knowland, K. Emma↗

NASA NTRS2019

Near Real-Time Air Quality Forecasts Using the NASA GEOS Model

Knowland, K. Emma↗

NASA NTRS2019

Near Real-Time Air Quality Forecasts Using the NASA GEOS Model

Knowland, K. Emma↗

NASA NTRS2019

Air Pollution Forecasts Using the NASA GEOS Model: A Unified Tool from Local to Global Scales

Knowland, K. Emma↗

NASA NTRS2012

Hydroclimatic Controls over Global Variations in Phenology and Carbon Flux

The connection between phenological and hydroclimatological variations are quantified through joint analyses of global NDVI, LAI, and precipitation datasets. The global distributions of both NDVI and LAI in the warm season are strongly controlled by three quantities: mean annual precipitation, the standard deviation of annual precipitation, and Budyko's index of dryness. Upon demonstrating that these same basic (if biased) relationships are produced by a dynamic vegetation model (the dynamic vegetation and carbon storage components of the NCAR Community Land Model version 4 combined with the water and energy balance framework of the Catchment Land Surface Model of the NASA Global Modeling and Assimilation Office), we use the model to perform a sensitivity study focusing on how phenology and carbon flux might respond to climatic change. The offline (decoupled from the atmosphere) simulations show us, for example, where on the globe a given small increment in precipitation mean or variability would have the greatest impact on carbon uptake. The analysis framework allows us in addition to quantify the degree to which climatic biases in a free-running GCM are manifested as biases in simulated phenology.

Koster, Randal↗

NASA NTRSDate not supplied

Near real-time air quality forecasts using the NASA GEOS model

NASA's Global Modeling and Assimilation Office (GMAO) produces high-resolution global forecasts for weather, aerosols, and air quality. The NASA Global Earth Observing System (GEOS) model has been expanded to provide global near-real-time5-day forecasts of atmospheric composition at unprecedented horizontal resolution of 0.25 degrees (~25 km). This composition forecast system (GEOS-CF) combines the operational GEOS weather forecasting model with the state-of-the-science GEOS-Chem chemistry module (version 12) to provide detailed analysis of a wide range of air pollutants such as ozone, carbon monoxide, nitrogen oxides, and fine particulate matter (PM2.5). Satellite observations are assimilated into the system for improved representation of weather and smoke. The assimilation system is being expanded to include chemically reactive trace gases. We discuss current capabilities of the GEOS Constituent Data Assimilation System (CoDAS) to improve atmospheric composition modeling and possible future directions, notably incorporating new observations (TROPOMI, geostationary satellites) and machine learning techniques. We show how machine learning techniques can be used to correct for sub-grid-scale variability, which further improves model estimates at a given observation site.

Air Quality Forecast↗

NASA NTRS2018

The SMAP Level-4 ECO Product - Phase 1: Improving Vegetation Simulations Through Observation-Driven Parameter Estimation

Simulations of hydrological fields as well as water, energy and carbon fluxes from the land surface to the atmosphere are crucial for a wide range of applications, including agricultural advisories, forecasts of (short-term) atmospheric behavior and seasonal weather predictions including forecasts of extreme events, such as heatwaves or droughts. The NASA Soil Moisture Active Passive (SMAP) mission Level-4 (L4) Eco-Hydrology (ECO) project aims to improve modeled estimates of the terrestrial water, energy and carbon fluxes and states by developing a fully-coupled hydrology-vegetation data assimilation (DA) algorithm. The DA system is developed for the NASA Goddard Earth Observing System version 5 (GEOS-5) Catchment-CN land surface model, which combines land hydrology components of the GEOS-5 Catchment model with dynamic vegetation components of the Community Land Model version 4. Catchment-CN fully couples the terrestrial water, energy and carbon cycles, allowing feedbacks from the land hydrology to the biosphere and vice versa. For SMAP L4 ECO a calibration of the Catchment-CN vegetation parameterization against observations of the fraction of absorbed photosynthetically active radiation (FPAR) from the Moderate Resolution Imaging Spectroradiometer (MODIS) is implemented to improve the model's standalone skill. Next, the DA algorithm used to produce the SMAP L4 soil moisture product is adapted to Catchment-CN to assimilate SMAP brightness temperatures and inform the model's land hydrology component. The DA system is further extended to assimilate MODIS FPAR observations in order to constrain the model's dynamic vegetation component. In this presentation, we demonstrate that the Catchment-CN parameter calibration leads to more realistic vegetation simulations and reduces the root mean squared error between modeled and observed vegetation states across the model's various plant functional types. We also show that the assimilation of SMAP observations is able to improve the average correlation, bias and unbiased RMSE between the modeled surface and root zone soil moisture estimates, and ground observations from the SMAP core validation sites.

Kolassa, J.↗

NASA NTRSDate not supplied

Benchmarking GOCART-2G in the Goddard Earth Observing System (GEOS)

The Goddard Chemistry Aerosol Radiation and Transport (GOCART) model, which controls the sources sinks and chemistry within the Goddard Earth Observing System, recently underwent a major refactoring and update to the representation of physical processes. The code refactoring increases flexibility such multiple instances of an aerosol species can be run and interact with radiation and cloud microphysics, in addition to the output of multiple wavelength aerosol optical properties in support of data assimilation. From a science perspective, a new radiatively active tracer, brown carbon, was added to distinguish smoke from other sources of organic aerosol thereby improving optical properties entering the radiative calculations. A four-year benchmark simulation was evaluated using in situ and space borne measurements to develop a baseline and prioritize future development. A comparison of simulated aerosol optical depth between GOCART-2G and MODIS retrievals indicates the model captures the overall spatial pattern and seasonal cycle of aerosol optical depth but overestimates aerosol extinction over dusty regions and underestimates aerosol extinction over northern hemisphere boreal forests, requiring further tuning of emissions. This MODIS-based analysis is corroborated by comparisons to MISR and selected AERONET stations. Despite the underestimate of aerosol optical depth in biomass burning regions in GEOS, there is an overestimate in the surface mass of organic carbon in the United States, especially during the summer months.

Allison Collow↗

NASA NTRS2024

Benchmarking GOCART-2G in the Goddard Earth Observing System (GEOS)

The Goddard Chemistry Aerosol Radiation and Transport (GOCART) model, which controls the sources sinks and chemistry within the Goddard Earth Observing System, recently underwent a major refactoring and update to the representation of physical processes. This paper serves to document code changes that were included in GOCART 2nd Generation (GOCART-2G) and establishes a benchmark simulation that is to be used for future development of the system. The code refactoring increases flexibility such multiple instances of an aerosol species can be run and interact with radiation and cloud microphysics, in addition to the output of multiple wavelength aerosol optical properties in support of data assimilation. From a science perspective, a new radiatively active tracer, brown carbon, was added to distinguish smoke from other sources of organic aerosol thereby improving optical properties entering the radiative calculations. A four-year benchmark simulation was evaluated using in situ and space borne measurements to develop a baseline and prioritize future development. A comparison of simulated aerosol optical depth between GOCART-2G and MODIS retrievals indicates the model captures the overall spatial pattern and seasonal cycle of aerosol optical depth but overestimates aerosol extinction over dusty regions and underestimates aerosol extinction over northern hemisphere boreal forests, requiring further tuning of emissions. This MODIS-based analysis is corroborated by comparisons to MISR and selected AERONET stations. Despite the underestimate of aerosol optical depth in biomass burning regions in GEOS, there is an overestimate in the surface mass of organic carbon in the United States, especially during the summer months.

Allison B Collow↗

NASA NTRS2018

Improving NASA GEOS Atmospheric CO2 Simulations by Calibrating CASA Surface Fluxes with an Empirical Sink

With the adoption of the Paris climate accord, efforts to monitor and understand both anthropogenic and natural carbon sources and sinks are increasing across the world. Given their low latency and global coverage, satellite observations of atmospheric carbon dioxide (CO2) are poised to make important contributions to this field. The combination of satellite data and high resolution global models can be used to monitor changes in carbon fluxes and to evaluate the consistency of nationally reported emissions estimates in support of multiple stakeholder communities. However, a consistent challenge to such work has been the high latency of surface carbon flux estimates, which are often not available for a year or more. This presentation describes the construction of surface carbon flux estimates meant to improve the near real time simulation of atmospheric CO2 with NASA's Goddard Earth Observing System (GEOS) general circulation model. The surface flux estimates begin with a collection of bottom-up fluxes which incorporate satellite measurements in their construction, e.g. vegetation indices in the Carnegie-Ames-Stanford Approach (CASA) and nighttime lights in the Open-source Data Inventory for Anthropogenic CO2 (ODIAC). From there, we take the additional step of using an empirical sink to calibrate terrestrial net biospheric exchange (NBE) to estimated values from atmospheric inversion systems. This approach removes a known, systematic bias in predicted atmospheric mixing ratios. Using these fluxes in a free running simulation, the model is able to reproduce in situ measurements with the same skill as when it uses gridded fluxes from a flux inversion system. Using these fluxes as a prior in an assimilation system, e.g. one incorporating retrievals of column CO2 from the Orbiting Carbon Observatory 2 (OCO-2), allows the analysis to capture variability in CO2 on scales that would be missed otherwise. This approach supports NASA's capability to forecast atmospheric CO2 up to two weeks in advance by leveraging a GEOS system used to produce quasi-operational weather analyses and forecasts, providing a valuable new tool to the carbon monitoring research and applications communities.

Weir, B.↗

NASA NTRS2015

The Quick Fire Emissions Dataset (QFED): Documentation of Versions 2.1, 2.2 and 2.4: Technical Report Series on Global Modeling and Data Assimilation - Volume 38

Biomass burning is an important source of particulates and trace gases and a major element of the terrestrial carbon cycle. Well constrained emissions from vegetation fires are needed to model direct and indirect effects of biomass burning aerosols, to model homogeneous and heterogeneous chemistry in the atmosphere, and to perform credible Earth system analysis, and climate and air pollution studies. To improve the performance of NASA Goddard Earth Observing System Model (GEOS) in the areas of atmospheric constituent modeling with a focus on biomass burning we developed the Quick Fire Emissions Dataset (QFED). The QFED emissions are based on the fire radiative power (top-down) approach and draw on the cloud correction method developed in the Global Fire Assimilation System (GFAS). Location and fire radiative power of fires are obtained from the Moderate Resolution Imaging Spectroradiometer (MODIS) Level 2 fire products (MOD14 and MYD14) and the MODIS Geolocation products (MOD03 and MYD03). QFED strengths are high spatial and temporal resolutions and near-real time availability. Daily mean emissions are available at 0.3125 times 0.25 degrees and in recent versions also at 0.1 times 0.1 degrees. QFED provides emissions of black carbon, organic carbon, sulfur dioxide, carbon monoxide, carbon dioxide, PM2.5, ammonia, nitrogen oxides, methyl ethyl ketone, propylene, ethane, propane, n- and i-butane, acetaldehyde, formaldehyde, acetone and methane. Two QFED product systems are maintained by the NASA Global Modeling and Assimilation Office (GMAO): one that produces near real-time daily emissions used operationally in the GEOS-5 Data Assimilation System, and one that produces an extended historical dataset with daily emissions from March 2000 to the present. The historical dataset also provides monthly mean and monthly climatological emissions.

Koster, Randal D.↗

NASA NTRS2014

Assimilation of Freeze - Thaw Observations into the NASA Catchment Land Surface Model

The land surface freeze-thaw (F-T) state plays a key role in the hydrological and carbon cycles and thus affects water and energy exchanges and vegetation productivity at the land surface. In this study, we developed an F-T assimilation algorithm for the NASA Goddard Earth Observing System, version 5 (GEOS-5) modeling and assimilation framework. The algorithm includes a newly developed observation operator that diagnoses the landscape F-T state in the GEOS-5 Catchment land surface model. The F-T analysis is a rule-based approach that adjusts Catchment model state variables in response to binary F-T observations, while also considering forecast and observation errors. A regional observing system simulation experiment was conducted using synthetically generated F-T observations. The assimilation of perfect (error-free) F-T observations reduced the root-mean-square errors (RMSE) of surface temperature and soil temperature by 0.206 C and 0.061 C, respectively, when compared to model estimates (equivalent to a relative RMSE reduction of 6.7 percent and 3.1 percent, respectively). For a maximum classification error (CEmax) of 10 percent in the synthetic F-T observations, the F-T assimilation reduced the RMSE of surface temperature and soil temperature by 0.178 C and 0.036 C, respectively. For CEmax=20 percent, the F-T assimilation still reduces the RMSE of model surface temperature estimates by 0.149 C but yields no improvement over the model soil temperature estimates. The F-T assimilation scheme is being developed to exploit planned operational F-T products from the NASA Soil Moisture Active Passive (SMAP) mission.

GEOS5↗