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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Sparsomycin inhibits translation through a conserved mechanism across all domains of life

Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

Paranjpe, Madhura N [Department of Biological Scie↗
DOE OSTI2021

Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome

In recent years, the root microbiome (i.e., microorganisms growing inside, on, or in close proximity to plant roots) has been shown to play an important role in plant health and productivity. Despite its importance, the root microbiome is challenging to study because of its complexity, heterogeneity, and subterranean location. Fortunately, root microbiome research has seen a tremendous influx of novel technologies (e.g., imaging tools, robotics, and molecular analyses), experimental platforms (e.g., micro- and mesocosms), and data integration, modeling, and prediction tools in the past decade that have greatly increased our ability to dissect the complex network of interactions between above- and belowground environmental parameters, plants, bacteria, and fungi that dictate soil and broader ecosystem health. Herein, we discuss methods that are currently used in root microbiome research and that can be expanded to phytobiome research in general ranging from laboratory studies to mesocosm-scale studies and, finally, to field studies; evaluate their relevance to ecosystem studies; and discuss future root microbiome research directions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Constraints and variation in food web link-species space

Predicting food web structure in future climates is a pressing goal of ecology. These predictions may be impossible without a solid understanding of the factors that structure current food webs. Here, the most fundamental aspect of food web structure—the relationship between the number of links and species—is still poorly understood. Some species interactions may be physically or physiologically ‘forbidden'—like consumption by non-consumer species—with possible consequences for food web structure. We show that accounting for these ‘forbidden interactions' constrains the feasible link-species space, in tight agreement with empirical data. Rather than following one particular scaling relationship, food webs are distributed throughout this space according to shared biotic and abiotic features. Our study provides new insights into the long-standing question of which factors determine this fundamental aspect of food web structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Localization crossover and subdiffusive transport in a classical facilitated network model of a disordered interacting quantum spin chain

Here, we consider the random-field Heisenberg model, a paradigmatic model for many-body localization (MBL) and add a Markovian dephasing bath coupled to the Anderson orbitals of the model's noninteracting limit. We map this system to a classical facilitated hopping model that is computationally tractable for large system sizes and investigate its dynamics. The classical model exhibits a robust crossover between an ergodic (thermal) phase and a frozen (localized) phase. The frozen phase is destabilized by thermal subregions (bubbles), which thermalize surrounding sites by providing a fluctuating interaction energy and so enable off-resonance particle transport. Investigating steady-state transport, we observe that the interplay between thermal and frozen bubbles leads to a clear transition between diffusive and subdiffusive regimes. This phenomenology both describes the MBL system coupled to a bath and provides a classical analog for the MBL transition in the corresponding quantum model, in that the classical model displays long local memory times. It also highlights the importance of the details of the bath coupling in studies of MBL systems coupled to thermal environments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae

Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. Here, we identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon.

09 BIOMASS FUELS↗
DOE OSTI2021

Global minimization via classical tunneling assisted by collective force field formation

Simple elements interacting in networks can give rise to intricate emergent behaviors. Examples such as synchronization and phase transitions often apply in many contexts, as many different systems may reduce to the same effective model. Here, we demonstrate such a behavior in a model inspired by memristors. When weakly driven, the system is described by movement in an effective potential, but when strongly driven, instabilities cause escapes from local minima, which can be interpreted as an unstable tunneling mechanism. We dub this collective and nonperturbative effect a “Lyapunov force,” which steers the system toward the global minimum of the potential function, even if the full system has a constellation of equilibrium points growing exponentially with the system size. This mechanism is appealing for its physical relevance in nanoscale physics and for its possible applications in optimization, Monte Carlo schemes, and machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth

Lipo-chitooligosaccharides (LCOs) are historically known for their role as microbial-derived signaling molecules that shape plant symbiosis with beneficial rhizobia or mycorrhizal fungi. Recent studies showing that LCOs are widespread across the fungal kingdom have raised questions about the ecological function of these compounds in organisms that do not form symbiotic relationships with plants. To elucidate the ecological function of these compounds, we investigate the metabolomic response of the ubiquitous human pathogen Aspergillus fumigatus to LCOs. Our metabolomics data revealed that exogenous application of various types of LCOs to A. fumigatus resulted in significant shifts in the fungal metabolic profile, with marked changes in the production of specialized metabolites known to mediate ecological interactions. Using network analyses, we identify specific types of LCOs with the most significant effect on the abundance of known metabolites. Extracts of several LCO-induced metabolic profiles significantly impact the growth rates of diverse bacterial species. These findings suggest that LCOs may play an important role in the competitive dynamics of non-plant-symbiotic fungi and bacteria. This study identifies specific metabolomic profiles induced by these ubiquitously produced chemicals and creates a foundation for future studies into the potential roles of LCOs as modulators of interkingdom competition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

LungMAP: The Molecular Atlas of Lung Development Program

The National Heart, Lung, and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic cross talk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis, and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have a significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults. A consortium of four research centers, a data coordinating center, and a human tissue repository provides high-quality molecular data of developing human and mouse lungs. LungMAP includes mouse and human data for cross correlation of developmental processes across species. LungMAP is generating foundational data and analysis, creating a web portal for presentation of results and public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology that incorporates the latest findings of the consortium. The LungMAP website (www.lungmap.net) currently contains more than 6,000 high-resolution lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers for young audiences. This paper presents a brief description of research conducted by the consortium, database, and portal development and upcoming features that will enhance the LungMAP experience for a community of users.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A simple and highly efficient protocol for 13 C-labeling of plant cell wall for structural and quantitative analyses via solid-state nuclear magnetic resonance

Plant cell walls are made of a complex network of interacting polymers that play a critical role in plant development and responses to environmental changes. Thus, improving plant biomass and fitness requires the elucidation of the structural organization of plant cell walls in their native environment. The 13 C-based multi-dimensional solid-state nuclear magnetic resonance (ssNMR) has been instrumental in revealing the structural information of plant cell walls through 2D and 3D correlation spectral analyses. However, the requirement of enriching plants with 13 C limits the applicability of this method. To our knowledge, there is only a very limited set of methods currently available that achieve high levels of 13 C-labeling of plant materials using 13 CO 2 , and most of them require large amounts of 13 CO 2 in larger growth chambers. In this study, a simplified protocol for 13C-labeling of plant materials is introduced that allows ca 60% labeling of the cell walls, as quantified by comparison with commercially labeled samples. This level of 13 C-enrichment is sufficient for all conventional 2D and 3D correlation ssNMR experiments for detailed analysis of plant cell wall structure. The protocol is based on a convenient and easy setup to supply both 13 C-labeled glucose and 13 CO 2 using a vacuum-desiccator. The protocol does not require large amounts of 13 CO 2 . This study shows that our 13 C-labeling of plant materials can make the accessibility to ssNMR technique easy and affordable. The derived high-resolution 2D and 3D correlation spectra are used to extract structural information of plant cell walls. This helps to better understand the influence of polysaccharide-polysaccharide interaction on plant performance and allows for a more precise parametrization of plant cell wall models.

09 BIOMASS FUELS↗
DOE OSTI2011

SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION

Protein phosphorylation and dephosphorylation play key roles in many aspects of plant biology, including control of cell division, pathways of carbon and nitrogen metabolism, pattern formation, hormonal responses, and abiotic and biotic responses to environmental signals. A Symposium on Plant Protein Phosphorylation was hosted on the Columbia campus of the University of Missouri from May 26-28, 2010. The symposium provided an interdisciplinary venue at which scholars studying protein modification, as it relates to a broad range of biological questions and using a variety of plant species, presented their research. It also provided a forum where current international challenges in studies related to protein phosphorylation could be examined. The symposium also stimulated research collaborations through interactions and networking among those in the research community and engaged students and early career investigators in studying issues in plant biology from an interdisciplinary perspective. The proposed symposium, which drew 165 researchers from 13 countries and 21 States, facilitated a rapid dissemination of acquired knowledge and technical expertise regarding protein phosphorylation in plants to a broad range of plant biologists worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor

Neutrons have historically been used for a broad range of biological applications employing techniques such as small-angle neutron scattering, neutron spin echo, diffraction, and inelastic scattering. Unlike neutron scattering techniques that obtain information in reciprocal space, attenuation-based neutron imaging measures a signal in real space that is resolved on the order of tens of micrometers. The principle of neutron imaging follows the Beer-Lambert law and is based on the measurement of the bulk neutron attenuation through a sample. Greater attenuation is exhibited by some light elements (most notably, hydrogen), which are major components of biological samples. Contrast agents such as deuterium, gadolinium, or lithium compounds can be used to enhance contrast in a similar fashion as it is done in medical imaging, including techniques such as optical imaging, magnetic resonance imaging, X-ray, and positron emission tomography. For biological systems, neutron radiography and computed tomography have increasingly been used to investigate the complexity of the underground plant root network, its interaction with soils, and the dynamics of water flux in situ. Moreover, efforts to understand contrast details in animal samples, such as soft tissues and bones, have been explored. This manuscript focuses on the advances in neutron bioimaging such as sample preparation, instrumentation, data acquisition strategy, and data analysis using the High Flux Isotope Reactor CG-1D neutron imaging beamline. The aforementioned capabilities will be illustrated using a selection of examples in plant physiology (herbaceous plant/root/soil system) and biomedical applications (rat femur and mouse lung).

Bilheux, Hassina↗
DOE OSTI2014

Ecological Principles and Guidelines for Managing the Use of Land

The many ways that people have used and managed land throughout history has emerged as a primary cause of land-cover change around the world. Thus, land use and land management increasingly represent a fundamental source of change in the global environment. Despite their global importance, however, many decisions about the management and use of land are made with scant attention to ecological impacts. Thus, ecologists' knowledge of the functioning of Earth's ecosystems is needed to broaden the scientific basis of decisions on land use and management. In response to this need, the Ecological Society of America established a committee to examine the ways that land-use decisions are made and the ways that ecologists could help inform those decisions. This paper reports the scientific findings of that committee. Five principles of ecological science have particular implications for land use and can assure that fundamental processes of Earth's ecosystems are sustained. These ecological principles deal with time, species, place, dis- turbance, and the landscape. The recognition that ecological processes occur within a temporal setting and change over time is fundamental to analyzing the effects of land use. In addition, individual species and networks of interacting species have strong and far-reaching effects on ecological processes. Furthermore, each site or region has a unique set of organisms and abiotic conditions influencing and constraining ecological processes. Distur- bances are important and ubiquitous ecological events whose effects may strongly influence population, com- munity, and ecosystem dynamics. Finally, the size, shape, and spatial relationships of habitat patches on the landscape affect the structure and function of ecosystems. The responses of the land to changes in use and management by people depend on expressions of these fundamental principles in nature. These principles dictate several guidelines for land use. The guidelines give practical rules of thumb for incorporating ecological principles into land-use decision making. These guidelines suggest that land managers should: (1) examine impacts of local decisions in a regional context, (2) plan for long-term change and unexpected events, (3) preserve rare landscape elements and associated species, (4) avoid land uses that deplete natural resources, (5) retain large contiguous or connected areas that contain critical habitats, (6) minimize the intro- duction and spread of nonnative species, (7) avoid or compensate for the effects of development on ecological processes, and (8) implement land-use and management practices that are compatible with the natural potential of the area. Decision makers and citizens are encouraged to consider these guidelines and to include ecological per- spectives in choices on how land is used and managed. The guidelines suggest actions required to develop the science needed by land managers.

Ecology↗
NASA NTRS1977

The navigation system of the JPL robot

The control structure of the JPL research robot and the operations of the navigation subsystem are discussed. The robot functions as a network of interacting concurrent processes distributed among several computers and coordinated by a central executive. The results of scene analysis are used to create a segmented terrain model in which surface regions are classified by traversibility. The model is used by a path planning algorithm, PATH, which uses tree search methods to find the optimal path to a goal. In PATH, the search space is defined dynamically as a consequence of node testing. Maze-solving and the use of an associative data base for context dependent node generation are also discussed. Execution of a planned path is accomplished by a feedback guidance process with automatic error recovery.

Thompson, A. M.↗
NASA NTRS1951

Preliminary Investigation of the Supersonic Flow Field Downstream of Wire-mesh Nozzles in a Constant-area Duct / Lawrence I. Gould

An investigation was conducted in a 3.4- by 3.4-inch duct to determine the characteristics of the supersonic flow downstream of four wire-mesh screen nozzles with nominal design Mach numbers in the range between 1.97 and 2.58. Two types of disturbances were observed in the flow field: a fine network of interacting expansion and compression waves which were formed immediately downstream of the screens and appeared to dissipate within 25 to 40 wave intersections; and relatively strong oblique shock waves that originated at the junctions of the screens and the walls and were reflected throughout the length of the duct. Regions of fairly uniform flow were found to exist. The total-pressure loss across the screens varied from 22 percent at Mach number 1.58 to 43 percent at Mach number 2.06.

WIND TUNNELS↗
NASA NTRS2006

Promoting Lifelong Ocean Education: Shaping Tomorrow's Earth Stewards and the Science and Technology Workforce

The coming ocean observing systems provide an unprecedented opportunity to change both the public perception of our oceans, and to inspire, captivate and motivate our children, our young adults and even our fellow adults to pursue careers allied with the oceans and to become stewards of our Planet's last unexplored environment. Education plans for the operational component, the Integrated Ocean Observing System (IOOS), and for the research component, Ocean Research Interactive Observatory Networks (ORION), are designed to take advantage of this opportunity. In both cases, community recommendations were developed within the context of the following assumptions: 1. Utilize research on how people learn, especially the four-pronged model of simultaneous learner-centered, knowledge-center, assessment-centered and community-centered learning 2. Strive for maximum impact on national needs in science and technology learning 3. Build on the best of what is already in place 4. Pay special attention to quality, sustainability, and scalability of efforts 5. Use partnerships across federal, state and local government, academia, and industry. Community recommendations for 100s and ORION education have much in common and offer the opportunity to create a coherent education effort allied with ocean observing systems. Both efforts focus on developing the science and technology workforce of the future, and the science and technology literacy of the public within the context of the Earth system and the role of the oceans and Great Lakes in that system. Both also recognize that an organized education infrastructure that supports sustainability and scalability of education efforts is required if ocean observing education efforts are to achieve a small but measurable improvement in either of these areas. Efforts have begun to develop the education infrastructure by beginning to form a community of educators from existing ocean and aquatic education networks and by exploring needs and issues associated with using ocean observing information assets in education. Likewise efforts are underway to address workforce issues by a systematic analysis of current and future workforce and educational needs. These activities will be described as will upcoming opportunities for the community to participate in these efforts.

Meeson, Blanche↗
NASA NTRS2006

Tools for Tomorrow's Science and Technology Workforce: MATE's 2006 ROV Competition Sets Students' Sights on Ocean Observing Systems

Teams participating in the 2006 ROV competition organized by the Marine Advanced Technology Education (MATE) Center and the Marine Technology Society's (MTS) ROV Committee experienced first-hand the scientific and technical challenges that many ocean scientists, technicians, and engineers face every day. The competition tasked more than 1,000 middle and high school, college, and university students from Newfoundland to Hong Kong with designing and building ROVs to support the next generation of ocean observing systems. Teaming up with the National Office for Integrated and Sustained Ocean Observations, Ocean. US, and the Ocean Research Interactive Observatory Networks (ORION) Program, the competition highlighted ocean observing systems and the careers, organizations, and technologies associated with ocean observatories. The student teams were challenged to develop vehicles that can deploy, install, and maintain networks of instruments as well as to explore the practical applications and the research questions made possible by observing systems.

OCEANOGRAPHERS↗