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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Expanding the genetic toolset: using serine recombinases to integrate riboregulatory elements into industrially relevant microbial chassis

To realize the full potential of biomanufacturing, the breadth of industrial microbes used to consume diverse feedstock and generate bioproducts needs to expand. As such, portable tools are required that can be used by multiple hosts for straightforward genomic manipulation and precise gene expression. Here, we demonstrate the co-utilization of two synthetic biology tools to achieve these goals: cis-repressors (CRs) and serine recombinase-assisted genome engineering (SAGE). CRs are small, noncoding RNAs that are placed upstream of the target gene to modulate bacterial translation rates at varying, discrete levels. SAGE uses site-specific serine recombinases to catalyze highly efficient, unidirectional insertion of DNA into the chromosome of diverse organisms. We used SAGE to integrate a suite of CRs into the industrially relevant hosts Pseudomonas putida, Corynebacterium glutamicum, and Cupriavidus necator. Using a fluorescent reporter as a readout of CR functionality, we found that CR performance across these backgrounds was similar—providing a range of translational repression up to 100-fold. Overall, these results demonstrate the high portability of CRs across bacterial genetic backgrounds, which ideally can be used in future microbial engineering efforts pertinent to biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Elements of Life, Photosynthesis and Genomics

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute’s efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets — focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors — that are well-used and appreciated by the community. Finally, a new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true “green yeast” and as a platform for engineering algae to produce useful bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Stationary Oxygen Vacancy Construction toward a Superior-Performance Ultrahigh Nickel Single-Crystal Cathode

Oxygen vacancies exert a complex and profound influence on the layered cathodes, especially those with ultrahigh nickel content. They can facilitate lithium-ion transport and enhance electronic conductivity, while aggressive oxygen vacancy formation causes structural degradation and electrolyte decomposition. Herein, taking ultrahigh nickel single-crystal LiNi 0.92 Co 0.06 Mn 0.02 O 2 (SC-Ni92) as a model material, we propose a pinning strategy to harness the benefits of oxygen vacancies while mitigating their detrimental effects. Through a carefully controlled thermal process, both oxygen vacancies and pinning atoms are successfully introduced into the surface region. The resulting anchored oxygen vacancies, capitalizing on their inherent advantages, improve conductivity and lithium-ion diffusion. Simultaneously, the neighboring pinning atoms effectively increase the migration barrier and suppress the adverse effects of these vacancies, including electrolyte decomposition and structural degradation during long-term electrochemical cycling. Consequently, oxygen vacancy-anchored single-crystal LiNi 0.92 Co 0.06 Mn 0.02 O 2 (SC-Ni92-OV) demonstrates significantly improved high-voltage electrochemical performance, with 86.16% capacity retention after 200 cycles at 4.6 V and 1 C in a half-cell and 90.71% after 300 cycles at 4.5 V and 1 C in a full cell. Furthermore, this study not only provides valuable insights into the chemistry of oxygen vacancy but also introduces a viable strategy for leveraging oxygen vacancies to achieve stable high-voltage performance in ultrahigh nickel single-crystal cathodes.

defects in solids↗
DOE OSTI2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery

Although the etiology of obesity is not well-understood, genetic, environmental, and microbiome elements are recognized as contributors to this rising pandemic. For morbid obesity, Roux-en-Y gastric bypass (RYGB) surgery alters the fecal microbiome, but data are sparse on temporal and spatial changes in the microbiome and metabolome. We characterized the structure and metabolism of the microbial communities in the gut lumen and on mucosal surfaces in morbidly obese individuals before and after RYGB surgery, and we compared our longitudinal cohort to a previously studied cross-sectional one. RYGB concurrently changed the gut microbiome and led to improvements of obesity comorbidities. Changes in the gut microbiome were reflected in the metabolome, including fermentation products and bile acids. The effects persisted 12 months post-surgery, and the microbiomes and metabolomes were similar to those found for the cross-sectional RYGB cohort. Thus, RYGB surgery had profound and persistent impacts on the intestinal microbiome and metabolome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Regulatory helix plays a key role in genetic ON-OFF switching for the 2’-deoxyguanosine sensing mRNA element

Transcriptional riboswitches, noncoding mRNA elements that operate in cis to regulate gene expression, have a promising potential in medicine, synthetic biology and directed evolution. They bind to cellular metabolites or metal ions with high specificity, leading to conformational rearrangements that facilitate the activation or premature termination of transcription for downstream genes. This elegant mechanism for feedback regulation of metabolic pathways has been identified in prokaryotes and a few in eukaryotes. Our chemical probing of the 2’-deoxyguanosine (2’-dG)-sensing riboswitch demonstrates that the overall conformational state of the full-length riboswitch (dGsw-fl) is unresponsive to the 2’-dG. Although binding proceeds as expected, dGsw-fl exclusively populates an OFF state of transcriptional inhibition. We chemically probed the structure of a known dGsw transcriptional intermediate (dGsw-int) to evaluate the possibility of a cotranscriptional regulatory role. Interestingly, apo dGsw-int adopts an alternative conformation in which a stable anti-terminator helix is formed, leading to an ON state where transcription can proceed. In the presence of 2’-dG, this anti-terminator helix is destabilized to produce a conformation reminiscent of the full-length, OFF-state dGsw. Using a fluorescence quenching assay, we demonstrate that binding 2’-dG to early transcriptional intermediates can inhibit the formation of the anti-terminator helix, locking dGsw in an OFF state. These data suggest that metabolite sensing occurs during a brief window of time between the synthesis of two transcriptional intermediates. Our studies indicate that dGsw does not function as a binary ON−OFF switch, but instead fine-tunes the transcription of downstream genes during RNA synthesis using key intermediates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Progress in Genetic Algorithm Fitting of X-Ray Fluorescence Data for Absorption Spectroscopy of Liquid Surfaces

X-ray fluorescence (XRF) spectroscopy of liquid surfaces is a promising approach to elemental analysis of forensic samples. Elements in the mixture can be identified from the XRF data because chemical elements are associated with unique spectra. This report describes progress in the development of automated identification of unknown mixtures of elements from XRF spectra using a genetic algorithm (GA). The XRF spectra are measured at the Advanced Photon Source (APS) at the liquid-liquid interface during solvent extraction process. The usage of the GA is demonstrated and future implementation for related problems are then discussed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation

Summary Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. In Arabidopsis , two enzymes share overlapping functions to produce TAGs, namely acyl‐CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in a dgat1‐1/pdat1‐2 double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue‐specific expression of either gene has not yet been identified. We transformed a dgat1‐1/dgat1‐1//PDAT1/pdat1‐2 parent with transgenic constructs containing the Arabidopsis DGAT1 promoter fused to the AtDGAT1 open reading frame either with or without the first intron. Triple homozygous plants were obtained, however, in the absence of the DGAT1 first intron anthers fail to fill with pollen, seed yield is c . 10% of wild‐type, seed oil content remains reduced (similar to dgat1‐1/dgat1‐1 ), and non‐Mendelian segregation of the PDAT1/pdat1‐2 locus occurs. Whereas plants expressing the AtDGAT1pro:AtDGAT1 transgene containing the first intron mostly recover phenotypes to wild‐type. This study establishes that a combination of the promoter and first intron of AtDGAT1 provides the proper context for temporal and tissue‐specific expression of AtDGAT1 in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes in Arabidopsis .

McGuire, Sean T.↗
DOE OSTI2021

The genetic architecture of leaf stable carbon isotope composition in Zea mays and the effect of transpiration efficiency on leaf elemental accumulation

With increased demand on freshwater resources for agriculture, it is imperative that more water-use efficient crops are developed. Leaf stable carbon isotope composition, δ 13 C, is a proxy for transpiration efficiency and a possible tool for breeders, but the underlying mechanisms effecting δ 13 C in C 4 plants are not known. It has been suggested that differences in specific leaf area (SLA), which potentially reflects variation in internal CO 2 diffusion, can impact leaf δ 13 C. Furthermore, although it is known that water movement is important for elemental uptake, it is not clear how manipulation of transpiration for increased water-use efficiency may impact nutrient accumulation. Here, we characterize the genetic architecture of leaf δ 13 C and test its relationship to SLA and the ionome in five populations of maize. Five significant QTL for leaf δ 13 C were identified, including novel QTL as well as some that were identified previously in maize kernels. One of the QTL regions contains an Erecta-like gene, the ortholog of which has been shown to regulate transpiration efficiency and leaf δ 13 C in Arabidopsis. QTL for δ 13 C were located in the same general chromosome region, but slightly shifted, when comparing data from two different years. Our data does not support a relationship between δ 13 C and SLA, and of the 19 elements analyzed, only a weak correlation between molybdenum and δ 13 C was detected. Together these data add to the genetic understanding of leaf δ 13 C in maize and suggest that improvements to plant water use may be possible without significantly influencing elemental homeostasis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

“CY1” Chondrites Produced by Impact Dehydration of the CI Chondrite Parent Body

The recently proposed Yamato-type (CY) chondrites share significant similarities with CI chondrites and Ryugu. We present major and trace elemental, Re–Os, and mass-independent Ti, Cr, and Fe isotope data for seven CY chondrites. The elemental data along with isotopic compositions reveal two distinct lithologies, here designated as CY1 and CY2, potentially originating from two different parent bodies. Although sharing similarities with CM chondrites, CY2 chondrites have distinct Cr isotope compositions, arguing against a close genetic relationship. The CY1 lithology exhibits elemental abundances similar to CI chondrites/Ryugu as well as Fe, Ti, and Cr isotope compositions that closely overlap with those of CI chondrites/Ryugu. This suggests that CI chondrites, CY1 chondrites, and Ryugu accreted in the same region of the solar system and may even originate from the same parent body. In fact, we find that the reduced water content and certain volatile element abundances alongside increased sulfide content and mass-dependent O isotope enrichments observed in CY1 compared to CI chondrites could be attributed to an impact-induced heating event on the CI parent body. This impact likely disrupted the CI parent body, resulting in the ejection of both CI and CY1 lithologies. Furthermore, given that there are presently only five known CI meteorite specimens, the close chemical composition between CY1 and CI chondrites substantially expands the data set for comparisons and referrals to the bulk solar system composition for nonvolatile elements. Finally, we propose that the “CY1” chondrites could be called “CI1T,” while the designation “CY” chondrites could be restricted to “CY2” samples.

Zhu, Ke 朱柯 [China University of Geosciences (Wuhan↗
DOE OSTI2021

Design of High Power Density 100 kW Surface Permanent Magnet Machine with No Heavy Rare Earth Material Using Current Source Inverter for Traction Application

Surface permanent magnet (SPM) machines are appealing candidates for traction applications because of high power density and high efficiency. Rare-earth magnets deliver high performance but raise concerns about material supply dependability, particularly if they use heavy rare-earth materials. This paper presents the design of a high-performance SPM machine without any heavy rare-earth material that is optimized specifically for a current-source inverter (CSI) traction drive. This machine is designed for a constant-power speed ratio (CPSR) of 3. A genetic algorithm has been performed to achieve a target of 50 kW/L active power density at speeds up to 20,000 rpm. Operation at a peak line-to-line voltage of 800 V can be achieved using 1200 V power devices with a safety margin. The predicted electromagnetic and rotor structural performance characteristics are presented using both analytical and finite element analysis (FEA) results.

(CPSR)↗
DOE OSTI2021

QTL × environment interactions underlie ionome divergence in switchgrass

Abstract Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species’ native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both the trait and QTL level. Concentrations of 14 of the 18 elements were under some genetic control, and 77 QTL were detected for these elements. Seventy-four percent of QTL colocalized multiple elements, half of QTL exhibited significant QTLxE, and roughly equal numbers of QTL had significant differences in magnitude and sign of their effects across environments. The switchgrass ionome is under moderate genetic control and by loci with highly variable effects across environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Summary Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Trace element geochemistry of coarse-grained angrites from Northwest Africa: Implications for their petrogenesis on the angrite parent body

The angrites are a class of achondrites that encompass a wide range of igneous textures from quenched, volcanic, and subvolcanic stones to slowly cooled, plutonic rocks. The compositions of the various geochemical reservoirs generating this variety of rocks have not been investigated fully because historically the numbers and masses of angrites available for study have been quite small. However, the rapid increase in meteorites from Northwest Africa (NWA) has enabled a renewed opportunity for such an investigation. In particular, three samples, NWA 2999, 4590, and 4801, have provided a new window into our understanding of the origin and petrogenesis of the coarse-grained (plutonic) angrites. We report here the trace element abundances in individual mineral grains of pyroxene, plagioclase, olivine/kirschsteinite, and phosphate and in the whole-rock samples. We utilize these data to constrain the petrogenetic history of each of these samples on the angrite parent body (e.g., parental melt compositions and oxygen fugacity conditions) and assess genetic relationships to previously investigated angrites. The trace element abundances in each of the three coarse-grained angrites studied here indicate a unique history for each. The observed trace element abundances and patterns in NWA 2999 show similarities with previously studied fine-grained, volcanic angrites and potentially indicate a common geochemical source reservoir, even though NWA 2999 is temporally distinct from the volcanic angrites. In contrast, NWA 4590 has trace element characteristics analogous to other coarse-grained angrites (e.g., Lewis Cliff [LEW] 86010), suggesting that these samples originated from geochemically similar source reservoirs. The third angrite, NWA 4801, exhibits geochemical characteristics most similar to the plutonic, coarse-grained angrites, but also appears to have some affinities in its trace element characteristics to the volcanic, fine-grained angrites. This suggests that NWA 4801 may represent a petrogenetic link between two distinct geochemical reservoirs on the angrite parent body. In aggregate, the trace element distributions in these three plutonic angrites suggest that while they may have originated up to several million years after the fine-grained angrites, they sampled a range of source reservoirs on the angrite parent body. Here, some of these source reservoirs were likely similar to those of the fine-grained angrites, but others had distinct geochemical characteristics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Design of a high power 8 MeV electron beam injector for the LERF

We present the beamline design for a high power 8 MeV electron injector to be installed at the Low Energy Recirculator Facility (LERF). The injector is designed to provide beam power of up to 80 kW for testing positron source target candidates. We discuss the results of beam dynamics simulations conducted using the General Particle Tracer (GPT) software, where electromagnetic beamline elements were optimized using multi-objective genetic algorithm tools. Additionally, we present preliminary studies on secondary particle generation from both rotating solid and free surface liquid metal jet targets described elsewhere in this workshop.

Lizarraga-Rubio, Victor [Thomas Jefferson National↗
DOE OSTI2026

Design of a high power 8 MeV electron beam injector for the LERF

Here, we present the beamline design for a high power 8 MeV electron injector to be installed at the Low Energy Recirculator Facility (LERF). The injector is designed to provide beam power of up to 80 kW for testing positron source target candidates. We discuss the results of beam dynamics simulations conducted using the General Particle Tracer (GPT) software, where electromagnetic beamline elements were optimized using multi-objective genetic algorithm tools. Additionally, we present preliminary studies on secondary particle generation from both rotating solid and free surface liquid metal jet targets described elsewhere in this workshop.

Lizarraga-Rubio, Victor Manuel [Thomas Jefferson N↗
DOE OSTI2022

Unconventional genetic code systems in archaea

Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗