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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 OSTI2021

A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers

Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. Anabaena sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, iAnC892, for this organism using annotations and content obtained from multiple databases. iAnC892 describes both the vegetative and heterocyst cell types found in the filaments of Anabaena sp. ATCC 33047. iAnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of iAnC892 reaction content with the GSM of Anabaena sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to iAnC892. iAnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N2 fixation. When used alongside the strain design algorithm, OptForce, iAnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Genetic Study of Nif -Associated Genes in a Hyperthermophilic Methanogen

Methanocaldococcus has been considered a model genus, but genetic tools have not been forthcoming until recently. Here, we develop and illustrate the utility of positive selection with either of two selective agents (simvastatin and neomycin), negative selection, generation of markerless in-frame deletion mutations, and genetic complementation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗
DOE OSTI2022

A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.

09 BIOMASS FUELS↗
DOE OSTI2025

Design of lightweight BCC multi-principal element alloys with enhanced hydrogen storage using a machine learning-driven genetic algorithm

Body-centered cubic (BCC) based multi-principal element alloy (MPEA) hydrides have demonstrated significant potential for compact and efficient hydrogen storage. In this work, we first leverage machine learning (ML) models to predict the hydrogen affinity, storage capacity and phase stability of BCC MPEAs, creating a unique hydrogen-to-metal (H/M) predictor for materials with unprecedented performance. We developed a metaheuristic optimizer high-throughput framework by interfacing ML models with a genetic algorithm for the accelerated search of {Mg, Al, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Nb, Mo} based lightweight BCC MPEAs with improved hydrogen storage characteristics. We report five new MPEAs with a predicted gravimetric hydrogen storage capacity of around 3.5 wt% or more, including Cr 0.09 Mg 0.73 Ti 0.18 (4.25 wt% H) and Cr 0.21 Nb 0.11 Ti 0.35 V 0.33 (3.5 wt% H). The electronic structure of the top-performing composition, Cr 0.09 Mg 0.73 Ti 0.18 , was analyzed using density functional theory (DFT) to understand the reasons for its improved hydrogen storage properties compared to TiFe (1.90 wt% H), LaNi 5 (1.37 wt% H) or BCC MPEAs like TiVNbCr (3.70 wt% H). Temperature-dependent molecular dynamics (MD) studies were further performed on optimized BCC MPEAs to qualitatively study hydrogen mobility and analyze the effect of different elemental composition on bulk hydrogen diffusion. Our findings demonstrate how a ML assisted genetic algorithm framework can be used for efficient search of stable, lightweight and cost-effective MPEAs while minimizing the need for expensive ab initio calculations.

DFT↗
DOE OSTI2025

A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN

Rust fungi comprise thousands of species, many of which cause disease on important crop plants. The flax rust fungus Melampsora lini has been a model species for the genetic dissection of plant immunity since the 1940s; however, the highly fragmented and incomplete reference genome has so far hindered progress in effector gene discovery. Here, we generated a fully phased, chromosome-scale assembly of the two nuclear genomes of M. lini strain CH5, resolving an additional 320 Mbp of the sequence. The 482-Mbp dikaryotic genome is at least 79% repetitive, with a large proportion (approximately 40%) of the genome comprising young, highly similar transposable elements. The assembly resolves the known effector gene loci, some of which carry complex duplications that were collapsed in the previous assembly. Using a genetic map followed by manual correction of gene models, we identified the AvrM3 and AvrN genes, which encode unusually large fungal effector proteins and trigger defense responses when co-expressed with the corresponding resistance genes. We located the genes linked to the tetrapolar mating system on chromosomes 4 and 9, but in contrast to the cereal rusts that have one pheromone receptor gene per haplotype, in flax rust, three pheromone receptor genes were found, with two of them closely linked on one haplotype. Taken together, we show that a high-quality assembly is crucial for resolving complex gene loci, and given the increasing number of fungal effectors of large size, the commonly applied criterion for effector candidates of being small proteins needs to be reconsidered.

Melampsora↗
DOE OSTI2022

Quantum model learning agent: characterisation of quantum systems through machine learning

Accurate models of real quantum systems are important for investigating their behaviour, yet are difficult to distil empirically. Here, we report an algorithm—the quantum model learning agent (QMLA)—to reverse engineer Hamiltonian descriptions of a target system. We test the performance of QMLA on a number of simulated experiments, demonstrating several mechanisms for the design of candidate Hamiltonian models and simultaneously entertaining numerous hypotheses about the nature of the physical interactions governing the system under study. QMLA is shown to identify the true model in the majority of instances, when provided with limited a priori information, and control of the experimental setup. Our protocol can explore Ising, Heisenberg and Hubbard families of models in parallel, reliably identifying the family which best describes the system dynamics. We demonstrate QMLA operating on large model spaces by incorporating a genetic algorithm to formulate new hypothetical models. The selection of models whose features propagate to the next generation is based upon an objective function inspired by the Elo rating scheme, typically used to rate competitors in games such as chess and football. In all instances, our protocol finds models that exhibit F 1 score ≥ 0.88 when compared with the true model, and it precisely identifies the true model in 72% of cases, whilst exploring a space of over 250 000 potential models. By testing which interactions actually occur in the target system, QMLA is a viable tool for both the exploration of fundamental physics and the characterisation and calibration of quantum devices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Are scenario projections overly optimistic about future yield progress?

Historical increases in agricultural production were achieved predominantly by large increases in agricultural productivity. Intensification of crop and livestock production also plays a key role in future projections of agricultural land use. Here, we assess and discuss projections of crop yields by global agricultural land-use and integrated assessment models. To evaluate these crop yield projections, we compare them to empirical data on attainable yields by employing a linear and plateauing continuation of observed attainable yield trends. While keeping in mind the uncertainties of attainable yields projections and future climate change impacts, we find that, on average for all cereals on the global level, global projected yields by 2050 remain below the attainable yields. Additionally, this is also true for future pathways with high technological progress and mitigation efforts, indicating that projected yield increases are not overly optimistic, even under systemic transformations. Furthermore, on a regional scale, we find that for developing regions, specifically for sub-Saharan Africa, projected yields stay well below attainable yields, indicating that the large yield gaps which could be closed through improved crop management, may also persist in the future. In OECD countries, in contrast, current yields are already close to attainable yields, and the projections approach or, for some models, even exceed attainable yields by 2050. This observation parallels research suggesting that future progress in attainable yields in developed regions will mainly have to be achieved through new crop varieties or genetic improvements. The models included in this study vary widely in their implementation of yield progress, which are often split into endogenous (crop management) improvements and exogenous (technological) trends. More detail and transparency are needed in these important elements of global yields and land use projections, and this paper discusses possibilities of better aligning agronomic understanding of yield gaps and yield potentials with modelling approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The Application of a Genetic Algorithm to the Optimization of a Mesoscale Model for Emergency Response

Besides solving the equations of momentum, heat, and moisture transport on the model grid, mesoscale weather models must account for subgrid-scale processes that affect the resolved model variables. These are simulated with model parameterizations, which often rely on values preset by the user. Such “free” model parameters, along with others set to initialize the model, are often poorly constrained, requiring that a user select each from a range of plausible values. Finding the values to optimize any forecasting tool can be accomplished with a search algorithm, and one such process—the genetic algorithm (GA)—has become especially popular. As applied to modeling, GAs represent a Darwinian process: an ensemble of simulations is run with a different set of parameter values for each member, and the members subsequently judged to be most accurate are selected as “parents” who pass their parameters onto a new generation. At the U.S. Department of Energy’s Savannah River Site in South Carolina, we are applying a GA to the Regional Atmospheric Modeling System (RAMS) mesoscale weather model, which supplies input to a model to simulate the dispersion of an airborne contaminant as part of the site’s emergency response preparations. An ensemble of forecasts is run each day, weather data are used to “score” the individual members of the ensemble, and the parameters from the best members are used for the next day’s forecasts. As meteorological conditions change, the parameters change as well, maintaining a model configuration that is best adapted to atmospheric conditions. Significance Statement We wanted to develop a forecasting system by which a weather model is run over the Savannah River Site each day and repeatedly adjusted according to how well it performed the previous day. To run the model, a series of values (parameters) must be set to control how the model will calculate winds, temperatures, and other desired variables. Each day the model was run several times using different combinations of these parameters and later compared with observed meteorological conditions. Parameters that produced the most accurate forecasts were preferentially reused to create the forecasts for the next day. The process was tested for the summer of 2020 and exhibited lower errors than forecasts produced by the model using default values of the parameters.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy

Irinotecan treats a range of solid tumors, but its effectiveness is severely limited by gastrointestinal (GI) tract toxicity caused by gut bacterial β-glucuronidase (GUS) enzymes. Targeted bacterial GUS inhibitors have been shown to partially alleviate irinotecan-induced GI tract damage and resultant diarrhea in mice. Here, we unravel the mechanistic basis for GI protection by gut microbial GUS inhibitors using in vivo models. We use in vitro, in fimo, and in vivo models to determine whether GUS inhibition alters the anticancer efficacy of irinotecan. We demonstrate that a single dose of irinotecan increases GI bacterial GUS activity in 1 d and reduces intestinal epithelial cell proliferation in 5 d, both blocked by a single dose of a GUS inhibitor. In a tumor xenograft model, GUS inhibition prevents intestinal toxicity and maintains the antitumor efficacy of irinotecan. Remarkably, GUS inhibitor also effectively blocks the striking irinotecan-induced bloom of Enterobacteriaceae in immune-deficient mice. In a genetically engineered mouse model of cancer, GUS inhibition alleviates gut damage, improves survival, and does not alter gut microbial composition; however, by allowing dose intensification, it dramatically improves irinotecan’s effectiveness, reducing tumors to a fraction of that achieved by irinotecan alone, while simultaneously promoting epithelial regeneration. These results indicate that targeted gut microbial enzyme inhibitors can improve cancer chemotherapeutic outcomes by protecting the gut epithelium from microbial dysbiosis and proliferative crypt damage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A susceptibility gene signature for ERBB2-driven mammary tumour development and metastasis in collaborative cross mice

Background: Deeper insights into ERBB2-driven cancers are essential to develop new treatment approaches for ERBB2+ breast cancers (BCs). We employed the Collaborative Cross (CC) mouse model to unearth genetic factors underpinning Erbb2-driven mammary tumour development and metastasis. Methods: 732 F1 hybrid female mice between FVB/N MMTV-Erbb2 and 30 CC strains were monitored for mammary tumour phenotypes. GWAS pinpointed SNPs that influence various tumour phenotypes. Multivariate analyses and models were used to construct the polygenic score and to develop a mouse tumour susceptibility gene signature (mTSGS), where the corresponding human ortholog was identified and designated as hTSGS. The importance and clinical value of hTSGS in human BC was evaluated using public datasets, encompassing TCGA, METABRIC, GSE96058, and I-SPY2 cohorts. The predictive power of mTSGS for response to chemotherapy was validated in vivo using genetically diverse MMTV-Erbb2 mice. Findings: Distinct variances in tumour onset, multiplicity, and metastatic patterns were observed in F1-hybrid female mice between FVB/N MMTV-Erbb2 and 30 CC strains. Besides lung metastasis, liver and kidney metastases emerged in specific CC strains. GWAS identified specific SNPs significantly associated with tumour onset, multiplicity, lung metastasis, and liver metastasis. Multivariate analyses flagged SNPs in 20 genes (Stx6, Ramp1, Traf3ip1, Nckap5, Pfkfb2, Trmt1l, Rprd1b, Rer1, Sepsecs, Rhobtb1, Tsen15, Abcc3, Arid5b, Tnr, Dock2, Tti1, Fam81a, Oxr1, Plxna2, and Tbc1d31) independently tied to various tumour characteristics, designated as a mTSGS. hTSGS scores (hTSGSS) based on their transcriptional level showed prognostic values, superseding clinical factors and PAM50 subtype across multiple human BC cohorts, and predicted pathological complete response independent of and superior to MammaPrint score in I-SPY2 study. The power of mTSGS score for predicting chemotherapy response was further validated in an in vivo mouse MMTV-Erbb2 model, showing that, like findings in human patients, mouse tumours with low mTSGS scores were most likely to respond to treatment. Interpretation: Our investigation has unveiled many new genes predisposing individuals to ERBB2-driven cancer. Translational findings indicate that hTSGS holds promise as a biomarker for refining treatment strategies for patients with BC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Genetic algorithm optimization of nuclear criticality experiment for reduction of intermediate-energy 239 Pu nuclear data uncertainties

Nuclear criticality experiments are conducted to investigate specific nuclear data important for safe handling and storage of fissile materials, reactor design and operation, and the validation of radiation transport codes. Incorrect or uncertain nuclear data can prohibitively impact operational safety limits, reactor licensing, and predictive simulation capability; therefore, integral measurements from criticality experiments are necessary and should be performed frequently. To maximize the impact of the integral measurements, it is important to consider experiment geometry, material selection, and component dimensions. When taking these considerations into account, the experiment design process becomes iterative and very time intensive. This work utilizes a genetic algorithm to efficiently explore potential nuclear criticality experiment designs for the Laboratory Directed Research & Development project PARADIGM (PARallel Approach of Differential and InteGral Measurements) at Los Alamos National Laboratory. In this paper, the building blocks of the genetic algorithm are discussed in detail, the genetic algorithm methodology is verified, and the genetic algorithm is used to produce three candidate experiment models for the final PARADIGM design. The three candidate models produced by the genetic algorithm consist of copper-reflected assemblies containing 14 repeating units of alumina, graphite, boron, and plutonium plates. Furthermore, in addition to the optimization results, final design considerations are also discussed for designs with a height and/or weight very close to or slightly above assembly machine operational limits.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Genetic tools for engineering Zymomonas mobilis , Cereibacter sphaeroides and Novosphingobium aromaticivorans to improve production of bioenergy compounds

Limited genetic tools for non-model bacteria are one of the limiting factors for genetic studies. This review compiles genetic tools used for three non-model alpha-proteobacteria, such as Zymomonas mobilis, Cereibacter (Rhodobacter) sphaeroides, and Novosphingobium aromaticivorans, which hold significant potential to produce industrially essential bioenergy compounds due to their distinctive metabolic pathways and resilience in extreme environments. Each of these strains has a unique genetic profile that enables them to efficiently carry out key reactions relevant to producing bioenergy compounds, such as converting sugars into bioenergy compounds and breaking down lignotoxins. Genetic tools can further optimize these strains for enhanced bioenergy compound production. This review explores the metabolic advantages of these organisms. It highlights the available array of genetic toolkits that can be shared among them to unlock their full potential for sustainable biofuel production.

Biofuel↗
DOE OSTI2023

The Genetics of Aerotolerant Growth in Zymomonas mobilis

Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium, Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most "generally essential" genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rnf respiratory complex are required for anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishes Z. mobilis as a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informs Z. mobilis genome manipulation for optimized production of valuable isoprenoid-based bioproducts

Alphaproteobacteria↗
DOE OSTI2023

The genetics of aerotolerant growth in an alphaproteobacterium with a naturally reduced genome

Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living alphaproteobacterium Zymomonas mobilis has a naturally reduced genome containing fewer than 2,000 protein-coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model alphaproteobacterium. Here, we use genome-scale CRISPRi-seq (clustered regularly interspaced short palindromic repeats interference sequencing) to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most “generally essential” genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as a reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rhodobacter nitrogen fixation (Rnf) respiratory complex are required for the anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishes Z. mobilis as a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informs Z. mobilis genome manipulation for optimized production of valuable isoprenoid-based bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Approaches to genetic tool development for rapid domestication of non-model microorganisms

Abstract Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, “domestication” of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.

09 BIOMASS FUELS↗
DOE OSTI2024

Correlated Anion Disorder in Heteroanionic Cubic TiOF 2

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO 3 -type) TiOF 2 using X-ray pair distribution function (PDF), 19 F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF 2 , characterized by predominant cis-[O 2 F 4 ] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19 F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19 F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF 4 . We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗