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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports large-scale data generation efforts across its two divisions: Biological Systems Science and Earth and Environmental Systems Sciences. These efforts include user facilities in atmospheric radiation measurements, genomics, metabolomics, proteomics, compute, and imaging. In addition, BER supports the development of plant-based fuels; research in biosystems design, environmental microbiomes, and atmospheric systems; energy flux monitoring; climate-based ecosystem experiments; pathogen biopreparedness; and modeling of climate, urban interfaces, and interactions between people and energy resources. For data access, BER supports community data services at its user facilities, along with specialized data initiatives for Earth and environmental science, climate modeling, genomic and microbial analysis, and multisector dynamics modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

All scales must be considered to understand rifts

Feedbacks between chemical, physical, and biological processes at rift zones evolve through various time (seconds to 10 7 yrs) and spatial (microns to 10 6 m) scales. Here, we discuss how consideration of these scales is needed to tap rift energy, water, and mineral resources safely and equitably while preserving biodiversity in these changing settings.

58 GEOSCIENCES↗
NASA NTRSDate not supplied

My Journey to NASA and role as a (Molecular) Biologist…

My journey to NASA started in undergrad, where I performed microbiology research and became hooked in the STEM fields. From there I earned a Ph.D. in Biochemistry and Molecular Biology from Mayo Graduate school where I performed Pancreatic Cancer research and then went on to perform postdoctoral research in Developmental Biology at the University of Miami. Trained as a biologist, I landed my first job at NASA as a mission scientist on the Rodent Research project. As a mission scientist, I led science activities associated with development, flight, and post-flight analysis of rodent research missions on the ISS in consultation with project engineers, operational specialists, mission PI(s), and mission Implementation Partner(s). I also assessed the feasibility of scientific experiments as a technical and scientific expert in rodent research on the ISS. Eager to learn more about the molecular changes that occur as a result of spaceflight exposure, I transitioned to the NASA GeneLab project where I eventually became the data processing lead. NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. To maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. During the CA Space Grant Women in STEM Panel event, I will provide an overview of my journey to NASA including my work at NASA on both the Rodent Research and GeneLab projects. I will conclude by providing resources for opportunities to work with GeneLab and NASA at large followed by links to programs designed specifically to engage women in STEM fields.

Amanda M Saravia-Butler↗
DOE OSTI2021

Omics-Lethal Human Viruses, Influenza A Experiment ICL105

The purpose of this experiment was to evaluate the host epigenetic response to Influenza A (H5N1) viral infection from human lung adenocarcinoma cells (Calu-3) high throughput sequencing (ChIP-Seq) sample data. Host-associated viral downloads contain one or more primary host-pathogen experimental study metadata design workbooks (supporting metadata only).

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

My Journey to NASA and Role as a (Molecular) Biologist…

My journey to NASA started in undergrad, where I performed microbiology research and became hooked in the STEM fields. From there I earned a Ph.D. in Biochemistry and Molecular Biology from Mayo Graduate school where I performed Pancreatic Cancer research and then went on to perform postdoctoral research in Developmental Biology at the University of Miami. Trained as a biologist, I landed my first job at NASA as a mission scientist on the Rodent Research project. As a mission scientist, I led science activities associated with development, flight, and post-flight analysis of rodent research missions on the ISS in consultation with project engineers, operational specialists, mission PI(s), and mission Implementation Partner(s). I also assessed the feasibility of scientific experiments as a technical and scientific expert in rodent research on the ISS. Eager to learn more about the molecular changes that occur as a result of spaceflight exposure, I transitioned to the NASA GeneLab project where I eventually became the data processing lead. NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. To maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. During the NASA Ames ECN at Lincoln HS Virtual Panel event, I will provide an overview of my journey to NASA including my work at NASA on both the Rodent Research and GeneLab projects. I will conclude by providing resources for opportunities to work with GeneLab and NASA at large followed by links to programs designed specifically to engage women in STEM fields.

Amanda M Saravia-Butler↗
NASA NTRS2015

Using Science Skills to Understand Ecophysiology and Manage Resources

Presentation will be for a general audience and focus on plant science and ecosystem science in NASA. Examples from the projects involving the presenter will be used to illustrate. Specifically, the California Sacramento-San Joaquin River Delta project. This collaboration supports the goals of the Delta Plan in developing science-based, adaptive-management strategies. The mission is to improve reliability of water supply and restore a healthy Delta ecosystem while enhancing agriculture and recreation. NASA can contribute gap-filling science understanding of overall functions in the Delta ecosystem and assess and help develop management plans for specific issues. Airborne and satellite remote-sensing, ecosystem modeling, and biological studies provide underlying data needed by Delta stakeholders to assess and address water, ecosystem restoration, and environmental and economic impacts of potential actions in the Delta. The California Sacramento-San Joaquin River Delta, the hub for California's water supply, supports important ecosystem services for fisheries, supplies drinking water for millions, and distributes water from Northern California to agriculture and urban communities to the south; millions of people and businesses depend on Delta water. Decades of competing demands for Delta resources and year-to-year variability in precipitation has resulted in diminished overall health of the Delta. Declines in fish populations, threatened ecosystems, endangered species, invasive plants and animals, cuts in agricultural exports, and increased water conservation is the result. NASA and the USDA, building on previous collaborations, aide local Delta stakeholders in assessing and developing an invasive weed management approach. Aquatic, terrestrial, and riparian invasive weeds threaten aquatic and terrestrial ecosystem restoration efforts. Aquatic weeds are currently detrimental economically, environmentally, and sociologically in the Delta. They negatively impact the redistribution of water and disrupt the ecology of the Bay Delta food web. Filling current science gaps in the Delta Plan and improving management practices within the Delta are important to achieving the mission of improved Delta health. Methods developed can become routine land and water management tools. New high-resolution NASA sensor systems could be used to provide data packages specifically designed for water system The presenter will also speak about his personal experience and the role Delaware Valley College played in preparation for a professional career science.

Water↗
NASA NTRS2010

Automated, Miniaturized Instrument for Measuring Gene Expression in Space

To facilitate astrobiological studies on the survival and adaptation of microorganisms and mixed microbial cultures to space environment, we have been developing a fully automated, miniaturized system for measuring their gene expression on small spacecraft. This low-cost, multi-purpose instrument represents a major scientific and technological advancement in our ability to study the impact of the space environment on biological systems by providing data on cellular metabolism and regulation orders of magnitude richer than what is currently available. The system supports growth of the organism, lyse it to release the expressed RNA, label the RNA, read the expression levels of a large number of genes by microarray analysis of labeled RNA and transmit the measurements to Earth. To measure gene expression we use microarray technology developed by CombiMatrix, which is based on electrochemical reactions on arrays of electrodes on a semiconductor substrate. Since the electrical integrity of the microarray remains intact after probe synthesis, the circuitry can be employed to sense nucleic acid binding at each electrode. CombiMatrix arrays can be sectored to allow multiple samples per chip. In addition, a single array can be used for several assays. The array has been integrated into an automated microfluidic cartridge that uses flexible reagent blisters and pinch pumping to move liquid reagents between chambers. The proposed instrument will help to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment, develop effective countermeasures against these effects, and test our ability to sustain and grow in space organisms that can be used for life support and in situ resource utilization during long-duration space exploration. The instrument is suitable for small satellite platforms, which provide frequent, low cost access to space. It can be also used on any other platform in space, including the ISS. It can be replicated and used with only small modifications in multiple biological experiments with a broad range of goals in mind.

Pohorille, A.↗
DOE OSTI2022

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ten simple rules for getting and giving credit for data

This article attempts to summarize current best practices that support the movement towards enabling researchers to cite and receive credit for their data. The authors are a small representation of the people and organizations trying to make this happen, and we acknowledge that it is not possible to capture all efforts behind this endeavor in 10 Simple Rules. We encourage interested readers to dive deeper by providing related resources along the way.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

Life science research in space - The Spacelab era

The events leading up to Spacelab mission 4, which is to be dedicated exclusively to life sciences experimentation in 1984-85, are described. Out of 400 experiment proposals initially received and assessed, 87 candidates were chosen for definition studies to identify the resources which would be required. These proposals addressed such problems encountered in previous space flights as space motion sickness, cardiovascular deconditioning and muscle wasting, calcium loss, and red cell mass reduction. Additional experiments were selected from bioengineering, plant physiology, and cell biology. Human subjects will consist of a Mission Specialist Astronaut and up to four Payload Specialists. Equipment to be used in experimentation includes biotelemetry systems, microscopes, cameras, centrifuges and refrigerators, all of which have been designed for use in weightless conditions. The 87 candidate experiments will be further reduced to about 20.

Farrell, R. M.↗
NASA NTRS2000

The State, Potential Distribution, and Biological Implications of Methane in the Martian Crust

The search for life on Mars has recently focused on its potential survival in deep (>2 km) subpermafrost aquifers where anaerobic bacteria, similar to those found in deep subsurface ecosystems on Earth, may have survived in an environment that has remained stable for billions of years. An anticipated by-product of this biological activity is methane. The detection of large deposits of methane gas and hydrate in the Martian cryosphere, or as emissions from deep fracture zones, would provide persuasive evidence of indigenous life and confirm the presence of a valuable in situ resource for use by future human explorers.

Max, Michael D.↗
DOE OSTI2022

HPC Molecular Simulation Tries Out a New GPU: Experiences on Early AMD Test Systems for the Frontier Supercomputer

Molecular simulation is an important tool for nu- merous efforts in physics, chemistry, and the biological sciences. Simulating molecular dynamics requires extremely rapid cal- culations to enable sufficient sampling of simulated temporal molecular processes. The Hewlett Packard Enterprise (HPE) Cray EX Frontier supercomputer installed at the Oak Ridge Leadership Computing Facility (OLCF) will provide an exascale resource for open science, and will feature graphics processing units (GPUs) from Advanced Micro Devices (AMD). The future LUMI supercomputer in Finland will be based on an HPE Cray EX platform as well. Here we test the ports of several widely used molecular dynamics packages that have each made substantial use of acceleration with NVIDIA GPUs, on Spock, the early Cray pre-Frontier testbed system at the OLCF which employs AMD GPUs. These programs are used extensively in industry for pharmaceutical and materials research, as well as academia, and are also frequently deployed on high-performance computing (HPC) systems, including national leadership HPC resources. We find that in general, performance is competitive and installation is straightforward, even at these early stages in a new GPU ecosystem. Our experiences point to an expanding arena for GPU vendors in HPC for molecular simulation.

Sedova, Ada↗
DOE OSTI2023

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

Abstract The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society’s pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Scoping review of Culex mosquito life history trait heterogeneity in response to temperature

Abstract Background Mosquitoes in the genus Culex are primary vectors in the US for West Nile virus (WNV) and other arboviruses. Climatic drivers such as temperature have differential effects on species-specific changes in mosquito range, distribution, and abundance, posing challenges for population modeling, disease forecasting, and subsequent public health decisions. Understanding these differences in underlying biological dynamics is crucial in the face of climate change. Methods We collected empirical data on thermal response for immature development rate, egg viability, oviposition, survival to adulthood, and adult lifespan for Culex pipiens, Cx. quinquefasciatus, Cx. tarsalis , and Cx. restuans from existing literature according to the PRISMA scoping review guidelines. Results We observed linear relationships with temperature for development rate and lifespan, and nonlinear relationships for survival and egg viability, with underlying variation between species. Optimal ranges and critical minima and maxima also appeared varied. To illustrate how model output can change with experimental input data from individual Culex species, we applied a modified equation for temperature-dependent mosquito type reproduction number for endemic spread of WNV among mosquitoes and observed different effects. Conclusions Current models often input theoretical parameters estimated from a single vector species; we show the need to implement the real-world heterogeneity in thermal response between species and present a useful data resource for researchers working toward that goal. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2014

Arctic Sea Ice in Transformation: A Review of Recent Observed Changes and Impacts on Biology and Human Activity

Sea ice in the Arctic is one of the most rapidly changing components of the global climate system. Over the past few decades, summer areal extent has declined over 30, and all months show statistically significant declining trends. New satellite missions and techniques have greatly expanded information on sea ice thickness, but many uncertainties remain in the satellite data and long-term records are sparse. However, thickness observations and other satellite-derived data indicate a 40 decline in thickness, due in large part to the loss of thicker, older ice cover. The changes in sea ice are happening faster than models have projected. With continued increasing temperatures, summer ice-free conditions are likely sometime in the coming decades, though there are substantial uncertainties in the exact timing and high interannual variability will remain as sea ice decreases. The changes in Arctic sea ice are already having an impact on flora and fauna in the Arctic. Some species will face increasing challenges in the future, while new habitat will open up for other species. The changes are also affecting peoples living and working in the Arctic. Native communities are facing challenges to their traditional ways of life, while new opportunities open for shipping, fishing, and natural resource extraction.

Sea Ice↗