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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

Abstract Background and Aims New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. Methods We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. Key Results Using sliding-window population genetic analyses we find that differentiation is concentrated within ‘islands’ of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. Conclusions We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth’s climate rapidly changes.

58 GEOSCIENCES↗
DOE OSTI2023

Exploring Plant Cis –Regulatory Elements at Single–Cell Resolution: Overcoming Biological and Computational Challenges to Advance Plant Research

Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall have limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Furthermore, advances in single cell epigenomics have revolutionized the field identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges and common pitfalls in analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conformer-specific photochemistry imaged in real space and time

Conformation-dependent dynamics play an important role in organic chemistry syntheses such as electrocyclic reactions, as well as in biological processes such as protein folding. However, current time-resolved experimental methods struggle to distinguish conformers from each other, and conformational isomerism is usually analyzed through reactant and product distributions. Using a combination of mega–electron volt ultrafast electron diffraction and quantum wave packet simulations, Champenois et al. directly followed the photochemical electrocyclic ring opening of the molecule α-phellandrene with femtosecond time resolution and confirmed that the transformation of a specific molecular conformer follows the famous Woodward-Hoffmann rules. The proposed method is potentially a powerful tool to follow conformer specificity in various organic and biological systems in real time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Enhanced alkaline hydrolysis and biodegradability studies of nitrocellulose-bearing missile propellant

Large amounts of energetic materials which have been accumulated over the years in various manufacturing and military installations must be disposed of in an environmentally sound manner. Historically, the method of choice for destruction of obsolete or aging energetic materials has been open burning or open detonation (OB/OD). This destruction approach has become undesirable due to air pollution problems. Therefore, there is a need for new technologies which will effectively and economically deal with the disposal of energetic materials. Along those lines, we have investigated a chemical/biological process for the safe destruction and disposal of a double base solid rocket propellant (AHH), which was used in several 8 inch projectile systems. The solid propellant is made of nitrocellulose and nitroglycerin as energetic components, two lead salts which act as ballistic modifiers, triacetin as a plasticizer and 2-Nitrodiphenylamine (2-NDPA) as a stabilizer. A process train is being developed to convert the organic components of the propellant to biodegradable products and remove the lead from the process stream. The solid propellant is first hydrolyzed through an enhanced alkaline hydrolysis process step. Following lead removal and neutralization, the digested liquor rich in nitrates and nitrites is found to be easily biodegradable. The digestion rate of the intact ground propellant as well as the release of nitrite and nitrate groups were substantially increased when ultrasound were supplied to the alkaline reaction medium compared to the conventional alkaline hydrolysis. The effects of reaction time, temperature, sodium hydroxide concentration and other relevant parameters on the digestion efficiency and biodegradability have been studied. The present work indicates that the AHH propellant can be disposed of safely with a combination of physiochemical and biological processes.

Sidhoum, Mohammed↗
DOE OSTI2022

Comparative and pangenomic analysis of the genus Streptomyces

Abstract Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Dormancy and Recovery Testing for Biological Wastewater Processors

Resource recovery and recycling waste streams to usable water via biological water processors is a plausible component of an integrated water purification system. Biological processing as a pretreatment can reduce the load of organic carbon and nitrogen compounds entering physiochemical systems downstream. Aerated hollow fiber membrane bioreactors, have been proposed and studied for a number of years as an approach for treating wastewater streams for space exploration.

Dormancy↗
NASA NTRS2001

Application of Fe Isotopes to the Search for Life and Habitable Planets

The relatively new field of Fe isotope geochemistry can make important contributions to tracing the geochemical cycling of Fe, which bears on issues such as metabolic processing of Fe, surface redox conditions, and development of planetary atmospheres and biospheres. It appears that Fe isotope fractionation in nature and the lab spans about 4 per mil (%) in Fe-56/Fe-54, and although this range is small, our new analytical methods produce a precision of +/- 0.05% on sample sizes as small as 100 ng (10(exp -7) g); this now provides us with a sufficient "signal-to-noise" ratio to make this isotope system useful. We review our work in three areas: 1) the terrestrial and lunar rock record, 2) experiments on inorganic fractionation, and 3) experiments involving biological processing of Fe. Additional information is contained in the original extended abstract.

Johnson, Clark M.↗
DOE OSTI2019

Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site

Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub’s C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at “exosites.” However, identification of such sites is typically empirical and particularly challenging in large molecular machines. In this work, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface

Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Sensing Plant Photosynthesis Using Solar-Induced Chlorophyll Fluorescence: From Chloroplasts to the Globe

Photosynthesis is the fundamental biological process that introduced oxygen into Earth's atmosphere and continues to power life, from the earliest single-celled organisms to entire global ecosystems. Yet, measuring photosynthesis across scales has been challenging because traditional techniques have not transcended scales. The emergence of remote-sensing techniques to measure solar-induced chlorophyll fluorescence (SIF) provides a unique approach to estimate photosynthesis across spatiotemporal scales, representing a new age for optical remote sensing to study photosynthesis and shaping the decades of satellite SIF research. Here, focusing on spatiotemporal scales, we review the mechanisms that drive the relationship between SIF and photosynthesis. Remotely sensed SIF is modulated by biological drivers, environmental drivers, the interaction between biological and environmental drivers, and the viewing geometry. Studying fluorescence at small scales provides the ecophysiological understanding needed to disentangle the biological and environmental drivers of SIF at larger scales. Leveraging progress in satellite SIF, future research should focus on cross-scale mechanistic understanding of the drivers of SIF and using SIF as a metric for plant function beyond photosynthesis.

ecophysiology↗
DOE OSTI2017

What Do Structures Tell Us About Chemokine Receptor Function and Antagonism?

Chemokines and their cell surface G protein–coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Controlling Protein Enrichment in Lipid Sponge Phase Droplets using SNAP–Tag Bioconjugation

All cells use organized lipid compartments to facilitate specific biological functions. Membrane-bound organelles create defined spatial environments that favor unique chemical reactions while isolating incompatible biological processes. Despite the fundamental role of cellular organelles, there is a scarcity of methods for preparing functional artificial lipid-based compartments. In this work, we demonstrate a robust bioconjugation system for sequestering proteins into zwitterionic lipid sponge phase droplets. Incorporation of benzylguanine (BG)-modified phospholipids that form stable covalent linkages with an O 6 -methylguanine DNA methyltransferase (SNAP-tag) fusion protein enables programmable control of protein capture. We show that this methodology can be used to anchor hydrophilic proteins at the lipid-aqueous interface, concentrating them within an accessible but protected chemical environment. SNAP-tag technology enables the integration of proteins that regulate complex biological functions in lipid sponge phase droplets, and should facilitate the development of advanced lipid-based artificial organelles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves

Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advanced Analysis of X-ray Fluorescence Measurements of the Interfacial Density of Eu Ions at Liquid–Liquid Interfaces for Solvent Back-Extraction

X-ray fluorescence near total reflection (XFNTR) is the primary technique used to measure the element-specific interfacial density of ions at liquid−liquid interfaces. Fluorescence from ions in the bulk liquids can complicate the determination of the interfacial density; consequently, measurements have been previously limited to samples without ions in the upper phase and with concentrations on the order of 10 μM or less in the lower phase. We modify the analysis of XFNTR data to account for ions in both bulk phases, then demonstrate its use in the context of rare-earth separations processes. In a model of ion stripping (i.e., back-extraction), dodecane solutions of di(2-ethylhexyl)- phosphoric acid (HDEHP) loaded with Eu(III) at the 1 mM level are placed in contact with either pure water or aqueous solutions of nitric or citric acid at pH 3. XFNTR measurements of equilibrated, quiescent samples reveal that citric acid solutions produce a disproportionately large depletion of ions from the interface compared to that from the bulk organic solution, whereas stripping by pure water or nitric acid solutions is negligible. As a result, this advance in the methodology of XFNTR may have broad applicability to the investigation of metal ions in chemical and biological processes at liquid−liquid interfaces.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis [plus supplementary information]

Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes. Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes . Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids.

09 BIOMASS FUELS↗
DOE OSTI2022

Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis

A variety of chemical and biological processes have been proposed for conversion of sustainable low-cost feedstocks into industrial products. Here, a biorefinery concept is formulated, modeled, and analyzed in which a naturally (hemi)cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii, is metabolically engineered to convert the carbohydrate content of lignocellulosic biomasses (i.e., soybean hulls, transgenic poplar) into green hydrogen and acetone. Experimental validation of C. bescii fermentative performance demonstrated 82% carbohydrate solubilization of soybean hulls and 55% for transgenic poplar. A detailed technical design, including equipment specifications, provides the basis for an economic analysis that establishes metabolic engineering targets. This robust industrial process leveraging metabolically engineered C. bescii yields 206 kg acetone and 25 kg H 2 per metric ton of soybean hull, or 174 kg acetone and 21 kg H 2 per metric ton transgenic poplar. Beyond this specific case, the model demonstrates industrial feasibility and economic advantages of thermophilic fermentation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2019

Nipah Virus-Like Particle Egress Is Modulated by Cytoskeletal and Vesicular Trafficking Pathways: a Validated Particle Proteomics Analysis

Classified as a biosafety level 4 (BSL4) select agent, Nipah virus (NiV) is a deadly henipavirus in the Paramyxoviridae family, with a nearly 75% mortality rate in humans, underscoring its global and animal health importance. Elucidating the process of viral particle production in host cells is imperative both for targeted drug design and viral particle-based vaccine development. However, little is understood concerning the functions of cellular machinery in paramyxoviral and henipaviral assembly and budding. Recent studies showed evidence for the involvement of multiple NiV proteins in viral particle formation, in contrast to the mechanisms understood for several paramyxoviruses as being reliant on the matrix (M) protein alone. Further, the levels and purposes of cellular factor incorporation into viral particles are largely unexplored for the paramyxoviruses. To better understand the involvement of cellular machinery and the major structural viral fusion (F), attachment (G), and matrix (M) proteins, we performed proteomics analyses on virus-like particles (VLPs) produced from several combinations of these NiV proteins. Our findings indicate that NiV VLPs incorporate vesicular trafficking and actin cytoskeletal factors. The involvement of these biological processes was validated by experiments indicating that the perturbation of key factors in these cellular processes substantially modulated viral particle formation. These effects were most impacted for NiV-F-modulated viral particle formation either autonomously or in combination with other NiV proteins, indicating that NiV-F budding relies heavily on these cellular processes. These findings indicate a significant involvement of the NiV fusion protein, vesicular trafficking, and actin cytoskeletal processes in efficient viral particle formation. Nipah virus is a zoonotic biosafety level 4 agent with high mortality rates in humans. The genus to which Nipah virus belongs, Henipavirus , includes five officially recognized pathogens; however, over 20 species have been identified in multiple continents within the last several years. As there are still no vaccines or treatments for NiV infection, elucidating its process of viral particle production is imperative both for targeted drug design as well as for particle-based vaccine development. Developments in high-throughput technologies make proteomic analysis of isolated viral particles a highly insightful approach to understanding the life cycle of pathogens such as Nipah virus.

59 BASIC BIOLOGICAL SCIENCES↗