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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The structure and interaction of polymers affects secondary cell wall banding patterns in Arabidopsis

Abstract Xylem tracheary elements (TEs) synthesize patterned secondary cell walls (SCWs) to reinforce against the negative pressure of water transport. VASCULAR-RELATED NAC-DOMAIN 7 (VND7) induces differentiation, accompanied by cellulose, xylan, and lignin deposition into banded domains. To investigate the effect of polymer biosynthesis mutations on SCW patterning, we developed a method to induce tracheary element transdifferentiation of isolated protoplasts, by transient transformation with VND7. Our data showed that proper xylan elongation is necessary for distinct cellulose bands, cellulose–xylan interactions are essential for coincident polymer patterns, and cellulose deposition is needed to override the intracellular organization that yields unique xylan patterns. These data indicate that a properly assembled cell wall network acts as a scaffold to direct polymer deposition into distinctly banded domains. We describe the transdifferentiation of protoplasts into TEs, providing an avenue to study patterned SCW biosynthesis in a tissue-free environment and in various mutant backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A continental scale analysis reveals widespread root bimodality

An improved understanding of root vertical distribution is crucial for assessing plant-soil-atmosphere interactions and their influence on the land carbon sink. Here, we analyze a continental-scale dataset of fine roots reaching 2 meters depth, spanning from Alaskan tundra to Puerto Rican forests. Contrary to the expectation that fine root abundance decays exponentially with depth, we found root bimodality at ~20% of 44 sites, with secondary biomass peaks often below 1m. Root bimodality was more likely in areas with low total fine root biomass and was more frequent in shrublands than grasslands. Notably, secondary peaks coincided with high soil nitrogen content at depth. Our analyses suggest that deep soil nutrients tend to be underexploited, while root bimodality offers plants a mechanism to tap into deep soil resources. Our findings add to the growing recognition that deep soil dynamics are systematically overlooked, and calls for more research attention to this deep frontier in the face of global environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Arabidopsis bZIP11 Is a Susceptibility Factor During Pseudomonas syringae Infection

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
NASA NTRS2017

Extravehicular Activity Operations Concepts Under Communication Latency and Bandwidth Constraints

The Biologic Analog Science Associated with Lava Terrains (BASALT) project is a multi-year program dedicated to iteratively develop, implement, and evaluate concepts of operations (ConOps) and supporting capabilities intended to enable and enhance human scientific exploration of Mars. This pa-per describes the planning, execution, and initial results from the first field deployment, referred to as BASALT-1, which consisted of a series of 10 simulated extravehicular activities (EVAs) on volcanic flows in Idaho's Craters of the Moon (COTM) National Monument. The ConOps and capabilities deployed and tested during BASALT-1 were based on previous NASA trade studies and analog testing. Our primary research question was whether those ConOps and capabilities work acceptably when performing real (non-simulated) biological and geological scientific exploration under 4 different Mars-to-Earth communication conditions: 5 and 15 min one-way light time (OWLT) communication latencies and low (0.512 Mb/s uplink, 1.54 Mb/s downlink) and high (5.0 Mb/s uplink, 10.0 Mb/s downlink) bandwidth conditions representing the lower and higher limits of technical communication capabilities currently proposed for future human exploration missions. The synthesized results of BASALT-1 with respect to the ConOps and capabilities assessment were derived from a variety of sources, including EVA task timing data, network analytic data, and subjective ratings and comments regarding the scientific and operational acceptability of the ConOp and the extent to which specific capabilities were enabling and enhancing, and are presented here. BASALT-1 established preliminary findings that baseline ConOp, software systems, and communication protocols were scientifically and operationally acceptable with minor improvements desired by the "Mars" extravehicular (EV) and intravehicular (IV) crewmembers, but unacceptable with improvements required by the "Earth" Mission Support Center. These data will provide a basis for guiding and prioritizing capability development for future BASALT deployments and, ultimately, future human exploration missions.

Beaton, Kara H.↗
DOE OSTI2021

A Modified Vegetation Photosynthesis and Respiration Model (VPRM) for the Eastern USA and Canada, Evaluated With Comparison to Atmospheric Observations and Other Biospheric Models

Atmospheric CO 2 measurements from a dense surface network can help to evaluate terrestrial biosphere model (TBM) simulations of Net Ecosystem Exchange (NEE) with two key benefits. First, gridded CO 2 flux estimates can be evaluated over regional scales, not possible using flux tower observations at discrete locations for model evaluation. Second, TBM ability to explain atmospheric CO 2 fluctuations due to the biosphere can be directly tested, an important objective for anthropogenic emissions monitoring using atmospheric observations. Here, we customize the Vegetation Photosynthesis and Respiration Model (VPRM) for an eastern North American domain with strong biological activity upwind of urban areas. Parameters are optimized using flux tower observations from a historical database with sites in (and near) the domain. In addition, the respiration model (originally a linear function of temperature) is modified to account for impacts of changing foliage, non-linear temperature, and water stress. Flux estimates from VPRM, the Carnegie-Ames-Stanford Approach (CASA) model and the Simple Biosphere Model v4 (SiB4), are convolved with footprints from atmospheric transport models for evaluation with CO 2 observations at 21 towers in the domain, with roughly half of the towers used here for the first time. Results show that the new respiration model in VPRM helps to correct a growing season sink bias in the atmosphere associated with underestimated summertime respiration using the original model with annual parameters. The new VPRM also better explains fine-scale atmospheric CO 2 variability compared to other TBMs, due to higher resolution diagnostic phenology, the new respiration model, domain-specific parameters, and high-quality input data sets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

Background: To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements. Results: We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells. Conclusions: The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.

3D printing↗
DOE OSTI2023

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer

Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number. The natural lanthanide-binding protein lanmodulin (LanM) is a sustainable alternative to conventional solvent-extraction-based separation. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM’s quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM’s greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.

36 MATERIALS SCIENCE↗
NASA NTRS2003

Variability in Ocean Color Associated with Phytoplankton and Terrigenous Matter: Time Series Measurements and Algorithm Development at the FRONT Site on the New England Continental Shelf

Fronts in the coastal ocean describe areas of strong horizontal gradients in both physical and biological properties associated with tidal mixing and freshwater estuarine output (e.g. Simpson, 1981 and O Donnell, 1993). Related gradients in optically important constituents mean that fronts can be observed from space as changes in ocean color as well as sea surface temperature (e.g., Dupouy et al., 1986). This research program is designed to determine which processes and optically important constituents must be considered to explain ocean color variations associated with coastal fronts on the New England continental shelf, in particular the National Ocean Partnership Program (NOPP) Front Resolving Observational Network with Telemetry (FRONT) site. This site is located at the mouth of Long Island sound and was selected after the analysis of 12 years of AVHRR data showed the region to be an area of strong frontal activity (Ullman and Cornillon, 1999). FRONT consists of a network of modem nodes that link bottom mounted Acoustic Doppler Current Profilers (ADCPs) and profiling arrays. At the center of the network is the Autonomous Vertically Profiling Plankton Observatory (AVPPO) (Thwaites et al. 1998). The AVPPO consists of buoyant sampling vehicle and a trawl-resistant bottom-mounted enclosure, which holds a winch, the vehicle (when not sampling), batteries, and controller. Three sampling systems are present on the vehicle, a video plankton recorder, a CTD with accessory sensors, and a suite of bio-optical sensors including Satlantic OCI-200 and OCR-200 spectral radiometers and a WetLabs ac-9 dual path absorption and attenuation meter. At preprogrammed times the vehicle is released, floats to the surface, and is then winched back into the enclosure with power and data connection maintained through the winch cable. Communication to shore is possible through a bottom cable and nearby surface telemetry buoy, equipped with a mobile modem, giving the capability for near-real time data transmission and interactive sampling control.

Morrison, John R.↗
DOE OSTI2020

Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break

Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding

Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone–sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone–sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

CO 2 fertilization of terrestrial photosynthesis inferred from site to global scales

Significance The magnitude of the CO 2 fertilization effect on terrestrial photosynthesis is uncertain because it is not directly observed and is subject to confounding effects of climatic variability. We apply three well-established eco-evolutionary optimality theories of gas exchange and photosynthesis, constraining the main processes of CO 2 fertilization using measurable variables. Using this framework, we provide robust observationally inferred evidence that a strong CO 2 fertilization effect is detectable in globally distributed eddy covariance networks. Applying our method to upscale photosynthesis globally, we find that the magnitude of the CO 2 fertilization effect is comparable to its in situ counterpart but highlight the potential for substantial underestimation of this effect in tropical forests for many reflectance-based satellite photosynthesis products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

De novo design of a homo-trimeric amantadine-binding protein

The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C 3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.

59 BASIC BIOLOGICAL SCIENCES↗