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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Pan-Arctic Vegetation Cover (PAVC) database v1.1

The Pan-Arctic Vegetation Cover (PAVC) database contains synthesized field-data observations of vegetation cover from 978 Arctic Alaska plots with observations from 2010 to 2021. The cover datasets contain plot data at both the plant functional type (PFT) and species-level resolution, with standardized PFT definitions and species names. We synthesized publicly available point-intercept and visual estimate plots from the Arctic Vegetation Archive of Alaska, the Alaska Vegetation Plots Database, the North Slope Science Catalog, and the National Ecological Observatory Network; as well as previously unpublished data from the Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic).Users will find four synthesized datasets, 4 associated data descriptor (dd) files, and 1 metadata file in the PAVC database:synthesized_species_fcover.csv contains fractional cover (fcover) for unique accepted species names, where names include vegetation identified at the family, genus, species, subspecies, and variety levels, as well as general functional types across all 5 data sources. The synthesized_species_fcover_dd.csv accompanies this dataset with header information.synthesized_pft_fcover.csv contains fcover for the following PFTs: non-vascular plants with lichen and bryophyte subcategories, trees with deciduous and evergreen subcategories, shrubs with deciduous and evergreen subcategories, graminoids (grasses), and forbs (herbaceous flowering plants) measured as total cover. Litter and “other” cover are also included as total cover. Additional “types” include water and bare ground, which were measured as top cover. The synthesized_pft_fcover_dd.csv accompanies this dataset with header information.species_pft_checklist.csv is a lookup table containing the translation from a dataset species name to an accepted species name and to a PFT. This table can be used to clarify our species to PFT adjudications, and to aid users in assigning their own PFTs. Any issues found in this checklist should be reported in the Issues tab of our github.survey_unit_information.csv contains auxiliary information about the plots synthesized in this database. It contains useful information for filtering plots of interest based on temporal, geospatial, and contextual information about the plot surveys.flmd.csv contains metadata information about each file in the database.This research was performed as a part of the NGEE Arctic project. The NGEE Arctic project was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1967

Study of life support systems for space missions exceeding one year in duration, phase 1A. Volume 2 - Mission studies

The study covered by this report is a continuation of the work conducted under ' contract NAS 2-3012, Study of Life Support Systems For Space Missions Exceeding One Year In Duration Phase I. The previous work compared biological and chemical food processing systems with a stored food system for hypothetical missions of from 10 to 100 men for one to three years. The follow-on work Phase IA, the subject of this report, reviewed new concepts for waste processing and food manufacture in the closed system such as wastes for radiation shielding, wastes for propulsion, glycerol synthesis using chromatographic reactors, glycerol synthesis using acetylene as an intermediate, animal links, the use of radiophosphors for algae illumination, and new biological system approaches. The most promising of these new concepts were combined with the food producing systems evolved in Phase I and compared for three specific model missions; Earth orbit, lunar and mars. The effects of spacecraft power penalty, leakage rate, radiation shielding requirements and extravehicular expendable requirements were assessed and a cost effectiveness analysis was completed for each mission. The cost analysis compared the launch cost savings of the advanced systems with the R&D costs required to produce a flight ready system. The study results indicate that systems using wastes for radiation shielding, leakage makeup, or EVA expendables are very competitive with the biological and chemical food systems for all missions. The stored food baseline system and wastes for propulsion ranked poorly in the comparison studies.

R. B. Jagow↗
DOE OSTI2020

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Check-Up of Planet Earth at the Turn of the Millennium: Anticipated New Phase in Earth Sciences

Langley's remarkable solar and lunar spectra collected from Mt. Whitney inspired Arrhenius to develop the first quantitative climate model in 1896. In 1999, NASA's Earth Observing AM Satellite (EOS-AM) will repeat Langley's experiment, but for the entire planet, thus pioneering calibrated spectral observations from space. Conceived in response to real environmental problems, EOS-AM, in conjunction with other international satellite efforts, will fill a major gap in current efforts by providing quantitative global data sets with a resolution of few kilometers on the physical, chemical and biological elements of the earth system. Thus, like Langley's data, EOS-AM can revolutionize climate research by inspiring a new generation of climate system models and enable us to assess the human impact on the environment.

Kaufman, Y. J.↗
DOE OSTI2020

Terrestrial Ecosystem Science (Flyer 2020)

A significant fraction of the carbon dioxide (CO 2 ) released to the atmosphere during energy production is taken up by terrestrial ecosystems. This carbon “sink” represents an important but poorly characterized buffer for offsetting the greenhouse gas effects of anthropogenic CO 2 emissions. Also unclear are the effects of related processes such as nutrient, water, and energy cycling—in addition to climate variability and change— on that uptake. Resolving the terrestrial biosphere’s role in the global carbon cycle is consequently a high priority for the Terrestrial Ecosystem Science (TES) program within the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER). Understanding the mechanisms and dynamics of ecosystem processes in the face of a changing climate is also essential for improving the representation of terrestrial ecosystems and climate feedbacks in Earth system models (ESMs). TES supports research to advance fundamental understanding of terrestrial ecosystems and their roles in a changing climate.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1998

The development of spaceflight experiments with Arabidopsis as a model system in gravitropism studies

Experiments with Arabidopsis have been developed for spaceflight studies in the European Space Agency's Biorack module. The Biorack is a multiuser facility that is flown on the United States Space Shuttle and serves as a small laboratory for studying cell and developmental biology in unicells, plants, and small invertebrates. The purpose of our spaceflight research was to investigate the starch-statolith model for gravity perception by studying wild-type (WT) and three starch-deficient mutants of Arabidopsis. Since spaceflight opportunities for biological experimentation are scarce, the extensive ground-based testing described in this paper is needed to ensure the success of a flight project. Therefore, the specific aims of our ground-based research were: (1) to modify the internal configuration of the flight hardware, which originally was designed for large lentil seeds, to accommodate small Arabidopsis seeds; (2) to maximize seed germination in the hardware; and (3) to develop favorable conditions in flight hardware for the growth and gravitropism of seedlings. The hardware has been modified, and growth conditions for Arabidopsis have been optimized. These experiments were successfully flown on two Space Shuttle missions in 1997.

STS-84 Shuttle Project↗
NASA NTRS1999

Check-Up of Planet Earth at the Turn of the Millennium: Contribution of EOS-Terra to a New Phase in Earth Sciences

Langley's remarkable solar and lunar spectra collected from Mt. Whitney inspired Arrhenius to develop the first quantitative climate model in 1896. In 1999, NASA's Earth Observing AM Satellite (EOS-Terra) will repeat Langley's experiment, but for the entire planet, thus pioneering a wide array of calibrated spectral observations from space of the Earth System. Conceived in response to real environmental problems, EOS-Terra, in conjunction with other international satellite efforts, will fill a major gap in current efforts by providing quantitative global data sets with a resolution of few kilometers on the physical, chemical and biological elements of the earth system. Thus, like Langley's data, EOS-Terra can revolutionize climate research by inspiring a new generation of climate system models and enable us to assess the human impact on the environment. In the talk I shall review the historical developments that brought to the Terra mission, its objectives and example of application to biomass burning.

Kaufman, Yoram↗
NASA NTRS1998

Evaluation of risk from space radiation with high-energy heavy ion beams

The most challenging radiation in space consists of fully ionized atomic elements with high energy for which only the few lowest energy ions can be stopped in shielding materials. The health risk from exposure to these ions and their secondary radiations generated in shield materials is poorly understood since there are few human data and a systematic study in relevant animal model systems has not been made. The accuracy of risk prediction is described as the major limiting factor in the management of space radiation risk. The expected impact of systematic studies is examined using the limited available biological data and models. Given the limitations of current predictions, models must be developed that are able to incorporate the required fundamental scientific data into accurate risk estimates. The important radiation components that can be provided for laboratory testing are identified. The use of ground-based accelerator beams to simulate space radiation is explained and quantitative scientific constraints on such facilities are derived. Three facilities, one each in the United States, in Germany and in Japan, currently have the partial capability to satisfy these constraints. A facility has been proposed using the Brookhaven National Laboratory Booster Synchrotron in the United States; in conjuction with other on-site accelerators, it will be able to provide the full range of heavy ion beams and energies required.

NASA Discipline Radiation Health↗
NASA NTRS2018

BioSentinel: An Adaptable Platform for Studying the Biological Effects of Deep Space Radiation

NASA's BioSentinel mission is a 6U nanosatellite with autonomous life support that will utilize the budding yeast Saccharomyces cerevisiae to study the DNA damage response to the deep space radiation environment. BioSentinel is planned to launch in 2019 as a secondary payload on the Space Launch System's first Exploration Mission (EM-1), and will undergo a lunar fly-by and enter heliocentric orbit after deployment. As the first biological mission beyond Low Earth Orbit (LEO) in nearly half a century, this mission will help fill critical gaps in knowledge about the effects of uniquely composed, chronic, low-flux deep space radiation on biological systems. Yeast is well-suited for this mission due to its desiccation tolerance and space-flight heritage. As a eukaryotic model organism, it also serves as a robust analog for human cells. Data gathered on this mission will thus inform us of the hazards involved in long-duration human exploration in deep space, and the protections necessary to mitigate them. Due to its low-cost, flexible and advanced technology, the 4U BioSensor payload contained within the nanosatellite is adaptable to other model microorganisms, exploration platforms and environments relevant to human exploration, such as the ISS, the Lunar Orbital Platform - Gateway and future lunar landers. In order to query the DNA damage response to deep space radiation, BioSentinel contains a wild type yeast strain as a positive control, and a radiation sensitive rad51 mutant strain that is defective for DNA repair. Yeast cells are desiccated in microfluidic cards, and rehydrated with growth medium and metabolic indicator dye at the desired time points during the mission. A thermal control system supports these stasis and growth states, and an optical system continuously measures cell growth and metabolism. An onboard radiation spectrometer and dosimeter allows us to correlate the dose, energy and particle-type of deep space radiation to the biological response. Data received from the deep space biosensor will be compared to control payloads on Earth and the ISS. Ongoing science testing for the BioSentinel project includes optimization for cell viability, desiccation tolerance, and long-term biocompatibility, as well as radiation experiments to understand the sensitivity and responsiveness of cells to varying radiation doses and particle types.

BioSentinel↗
NASA NTRS2000

The Earth Observing System Terra Mission

Langley's remarkable solar and lunar spectra collected from Mt. Whitney inspired Arrhenius to develop the first quantitative climate model in 1896. After the launch in Dec. 16 1999, NASA's Earth Observing AM Satellite (EOS-Terra) will repeat Langley's experiment, but for the entire planet, thus pioneering a wide array of calibrated spectral observations from space of the Earth System. Conceived in response to real environmental problems, EOS-Terra, in conjunction with other international satellite efforts, will fill a major gap in current efforts by providing quantitative global data sets with a resolution smaller than 1 km on the physical, chemical and biological elements of the earth system. Thus, like Langley's data, EOS-Terra can revolutionize climate research by inspiring a new generation of climate system models and enable us to assess the human impact on the environment. In the talk I shall review the historical perspective of the Terra mission and the key new elements of the mission. We expect to have some first images that demonstrate the most innovative capability from EOS Terra: MODIS - 1.37 microns cirrus channel; 250 m daily cover for clouds and vegetation change; 7 solar channels for land and aerosol; new fire channels; Chlorophyll fluorescence; MISR - 9 multi angle views of clouds and vegetation; MOPITT - Global CO maps and CH4 maps; ASTER - Thermal channels for geological studies with 15-90 m resolution.

Kaufman, Yoram J.↗
NASA NTRS2000

The Earth Observing System Terra Mission

Langley's remarkable solar and lunar spectra collected from Mt. Whitney inspired Arrhenius to develop the first quantitative climate model in 1896. After the launch in Dec. 16 1999, NASA's Earth Observing AM Satellite (EOS-Terra) will repeat Langley's experiment, but for the entire planet, thus pioneering a wide array of calibrated spectral observations from space of the Earth System. Conceived in response to real environmental problems, EOS-Terra, in conjunction with other international satellite efforts, will fill a major gap in current efforts by providing quantitative global data sets with a resolution better than 1 km on the physical, chemical and biological elements of the earth system. Thus, like Langley's data, EOS-Terra can revolutionize climate research by inspiring a new generation of climate system models and enable us to assess the human impact on the environment. In the talk I shall review the historical perspective of the Terra mission and the key new elements of the mission. We expect to have first images that demonstrate the most innovative capability from EOS Terra 5 instruments: MODIS - 1.37 micron cirrus cloud channel; 250m daily coverage for clouds and vegetation change; 7 solar channels for land and aerosol studies; new fire channels; Chlorophyll fluorescence; MISR - first 9 multi angle views of clouds and vegetation; MOPITT - first global CO maps and C114 maps; ASTER - Thermal channels for geological studies with 15-90 m resolution.

Kaufman, Yoram J.↗
NASA NTRS2006

Radiation-Induced Leukemia at Doses Relevant to Radiation Therapy: Modeling Mechanisms and Estimating Risks

Because many cancer patients are diagnosed earlier and live longer than in the past, second cancers induced by radiation therapy have become a clinically significant issue. An earlier biologically based model that was designed to estimate risks of high-dose radiation induced solid cancers included initiation of stem cells to a premalignant state, inactivation of stem cells at high radiation doses, and proliferation of stem cells during cellular repopulation after inactivation. This earlier model predicted the risks of solid tumors induced by radiation therapy but overestimated the corresponding leukemia risks. Methods: To extend the model to radiation-induced leukemias, we analyzed in addition to cellular initiation, inactivation, and proliferation a repopulation mechanism specific to the hematopoietic system: long-range migration through the blood stream of hematopoietic stem cells (HSCs) from distant locations. Parameters for the model were derived from HSC biologic data in the literature and from leukemia risks among atomic bomb survivors v^ ho were subjected to much lower radiation doses. Results: Proliferating HSCs that migrate from sites distant from the high-dose region include few preleukemic HSCs, thus decreasing the high-dose leukemia risk. The extended model for leukemia provides risk estimates that are consistent with epidemiologic data for leukemia risk associated with radiation therapy over a wide dose range. For example, when applied to an earlier case-control study of 110000 women undergoing radiotherapy for uterine cancer, the model predicted an excess relative risk (ERR) of 1.9 for leukemia among women who received a large inhomogeneous fractionated external beam dose to the bone marrow (mean = 14.9 Gy), consistent with the measured ERR (2.0, 95% confidence interval [CI] = 0.2 to 6.4; from 3.6 cases expected and 11 cases observed). As a corresponding example for brachytherapy, the predicted ERR of 0.80 among women who received an inhomogeneous low-dose-rate dose to the bone marrow (mean = 2.5 Gy) was consistent with the measured ERR (0.62, 95% Cl =-0.2 to 1.9). Conclusions: An extended, biologically based model for leukemia that includes HSC initiation, inactivation, proliferation, and, uniquely for leukemia, long-range HSC migration predicts, %Kith reasonable accuracy, risks for radiationinduced leukemia associated with exposure to therapeutic doses of radiation.

Shuryak, Igor↗
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
NASA NTRS1999

Check-Up of Planet Earth at the Turn of the Millennium Anticipated New Phase in Earth Sciences

Langley's remarkable solar and lunar spectra collected from mt. Whitney inspired Arrhenius to develop the first quantitative climate model in 1896. In 1999, NASA's Earth Observing AM Satellite named recently "Terra" (by Ms. Sasha Jones, a 17 year old student in St. Louis, MO) will repeat Langley's experiment, but for the entire planet, thus pioneering calibrated spectral observations from space. Conceived in response to real environmental problems, EOS-AM, in conjunction with other international satellite efforts, will fill a major gap in current efforts by providing quantitative global data sets with a resolution of few kilometers on the physical, chemical and biological elements of the earth system. Thus, like Langley's data, EOS-AM can revolutionize climate research by inspiring a new generation of climate system models and enable us to assess the human impact on the environment. In this talk I shall a give a historical perspective for the need for this expensive mission, give examples of the science that we anticipate to achieve using Terra measurements and describe this exciting mission.

Kaufman, Yoram↗
NASA NTRS2008

NASA's Modern Era Retrospective-Analysis for Research and Applications (MERRA): Early Results and Future Directions

This talk will review the status and progress of the NASA/Global Modeling and Assimilation Office (GMAO) atmospheric global reanalysis project called the Modern Era Retrospective-Analysis for Research and Applications (MERRA). An overview of NASA's emerging capabilities for assimilating a variety of other Earth Science observations of the land, ocean, and atmospheric constituents will also be presented. MERRA supports NASA Earth science by synthesizing the current suite of research satellite observations in a climate data context (covering the period 1979-present), and by providing the science and applications communities with of a broad range of weather and climate data with an emphasis on improved estimates of the hydrological cycle. MERRA is based on a major new version of the Goddard Earth Observing System Data Assimilation System (GEOS-5), that includes the Earth System Modeling Framework (ESMF)-based GEOS-5 atmospheric general circulation model and the new NOAA National Centers for Environmental Prediction (NCEP) unified grid-point statistical interpolation (GST) analysis scheme developed as a collaborative effort between NCEP and the GMAO. In addition to MERRA, the GMAO is developing new capabilities in aerosol and constituent assimilation, ocean, ocean biology, and land surface assimilation. This includes the development of an assimilation capability for tropospheric air quality monitoring and prediction, the development of a carbon-cycle modeling and assimilation system, and an ocean data assimilation system for use in coupled short-term climate forecasting.

Schubert, Siegfried↗
DOE OSTI2020

A machine learning Automated Recommendation Tool for synthetic biology

Abstract Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Motility of acoustically powered micro-swimmers in a liquid crystalline environment

Suspensions of microswimmers in liquid crystals demonstrate remarkably complex dynamics and serve as a model system for studying active nematics. So far, experimental realization of microswimmers suspended in liquid crystalline media has relied on biological microorganisms that impose strict limitations on the compatible media and makes it difficult to regulate activity. Here, we demonstrate that acoustically powered bubble microswimmers can efficiently self-propel in a lyotropic liquid crystal. The velocity of the swimmers is controlled by the amplitude of the acoustic field. Histograms of swimming directions with respect to the local nematic field reveal a bimodal distribution: the swimmers tend to either fully align with or swim perpendicular to the director field of the liquid crystal, occasionally switching between these two states. The bubble-induced streaming from a swimmer locally melts the liquid crystal and produces topological defects at the tail of the swimmer. Further, we show that the defect proliferation rate increases with the angle between the swimmer's velocity and the local orientation of the director field.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A multi-modal scanning system to digitize CBRNE emergency response scenes

A handheld system developed to digitize a contextual understanding of the scene at a chemical, biological, radiological, nuclear and/or explosives (CBRNE) events is described. The system uses LiDAR and cameras to create a colorized 3D model of the environment, which helps domain experts that are supporting responders in the field. To generate the digitized model, a responder scans any suspicious objects and the surroundings by carrying the system through the scene. The scanning system provides a real-time user interface to inform the user about scanning progress and to indicate any areas that may have been missed either by the LiDAR sensors or the cameras. Currently, the collected data are post-processed on a different device, building a colorized triangular mesh of the encountered scene, with the intention of moving this pipeline to the scanner at a later point. The mesh is sufficiently compressed to be sent over a reduced bandwidth connection to a remote analyst. Furthermore, the system tracks fiducial markers attached to diagnostic equipment that is placed around the suspicious object. The resulting tracking information can be transmitted to remote analysts to further facilitate their supporting efforts. The paper will discuss the system's design, software components, the user interface used for scanning a scene, the necessary procedures for calibration of the sensors, and the processing steps of the resulting data. The discussion will close by evaluating the system's performance on 11 scenes.

Salathe, Marco↗