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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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516 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae

Introduction: Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. Methods: The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. Results: The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. Discussion: This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

09 BIOMASS FUELS↗
DOE OSTI2026

Optimizing resource allocation in Miscanthus breeding via sparse testing designs for genomic prediction

Phenotyping high-biomass perennial crops is laborious and the rate of genetic gain in conventional perennial crop breeding programs is typically low. So, it is especially important to identify methods that produce efficiency gains in the breeding process. Miscanthus is a C4 perennial grass with favorable characteristics for producing biomass as a feedstock for biofuels and diverse bio-based products. Increasing biomass yield will increase profitability and environmental benefits, so it is a key target for Miscanthus breeding. In addition, the identification of well-adapted genotypes across a wide range of environmental conditions requires the establishment of multi-environment trials (METs). Sparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations. A Miscanthus sacchariflorus (MSA) population comprising 336 genotypes observed across three environments was analyzed implementing sparse testing designs. Three prediction models considering main effects (environments, genotypes, genomic) and interaction effects (genotype-by-environment; G×E interaction) were implemented for forecasting dry biomass yield (YDY), total culm (TCM), average internode length (AIL), and culm node number (CNN). Multiple calibration sets based on different compositions and sizes were considered to evaluate performance in terms of the predictive ability (PA) and the mean square error (MSE) for a fixed testing set size. The training set size ranged from 52 to 112 to predict a fixed set of 224 unobserved genotypes across all three environments. The results showed that the model accounting for G×E interaction consistently presented the highest PA and the lowest MSE: for CNN (PA: ~0.77, MSE: ~0.5) and YDY (PA: ~0.70, MSE: ~1.3) while for TCM and AIL these ranged from ~0.28 to 0.41 and ~1.3 to 4.3, respectively. Overall, varying training sets and allocation strategies did not affect PA and MSE, with 52 non-overlapping and 0 overlapping genotypes per environment as the optimal cost-effective allocation framework. This suggests that implementing sparse testing designs could significantly reduce phenotyping costs by fivefold, without compromising PA in breeding programs for perennial crops such as Miscanthus.

Miscanthus sacchariflorus (MSA)↗
DOE OSTI2026

Multi-trait multi-environment genomic prediction strategies for Miscanthus sacchariflorus

Genomic selection holds the potential to serve as a strategic tool to enhance the genetic gain of complex traits in Miscanthus breeding programs. The development of improved cultivars requires their assessment for various traits across diverse environments to ensure suitable overall performance. Hence, the multi-trait multi-environment (MTME) genomic prediction (GP) models offer an opportunity to improve selection accuracy. This study aims to evaluate the potential of five GP models: (1) three MTME models including genotype-by-trait-by-environment interaction (G×E×T) and (2) two single-trait multi-environment (STME) models (with and without G×E interaction). A Miscanthus sacchariflorus population comprising 336 genotypes evaluated in three environments and scored for four traits (biomass yield YDY, total culm number TCM, average internode length AIL, and culm node number CNN) was analyzed. The predictive ability of the models was evaluated considering three cross-validation schemes resembling realistic scenarios (CV1: predicting new genotypes, CVP: predicting missing traits in a given environment, and CV2: predicting partially observed genotypes). On average, in all cross-validation schemes compared to the STME the predictive ability of the MTME models was 10% to 70% higher for TCM and AIL. On the other hand, for YDY and CNN, both STME models performed similarly or slightly better (between 5 to 64%) than the MTME models in most environments. While the MTME models were not successful for all traits when compared to their STME counterparts, MTME models improved the prediction of the performance of genotypes that were untested across environments or lacked trait information in a specific environment. Overall, our study suggests that MTME GP models can be implemented in Miscanthus breeding programs to improve the predictive ability of the complex traits, shorten breeding cycles, and accelerate selection decisions.

genomic prediction (GP)↗
DOE OSTI2025

Hepatocellular Metabolic Profile: Understanding Post-Thawing Metabolic Shift in Primary Hepatocytes In Vitro

Primary human hepatocytes (PHHs) are widely used as in vitro models for liver function and drug metabolism studies, yet their metabolic stability post-thawing remains an open question. To better characterize early metabolic changes, we conducted a time-course experiment using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze metabolic shifts in PHHs cultured in suspension. Unexposed and exposed (acetaminophen-treated) samples were evaluated, and TITAN analysis was applied to determine the time point of maximal metabolic change at both individual metabolite and global metabolic profile levels. Our results indicate that the majority of metabolic shifts occur within the first five hours post-thawing. In the early culture time points, substantial metabolic overlap was observed between unexposed and exposed cells, suggesting a conserved biological response likely related to cellular recovery. However, at later time points, metabolite profiles diverged, with acetaminophen treatment-specific metabolic changes emerging, potentially reflecting differences in homeostatic restoration versus hepatotoxic responses. Our study highlights the importance of considering early post-thawing metabolic dynamics in experimental design and offers insights for optimizing hepatocyte culture protocols to better replicate in vivo physiological conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Handling and Properties of Methanol as a Marine Fuel

Given the increasing concern around greenhouse gas emissions and the decline in the availability of fossil fuels, there is increasing global demand to develop alternate fuels for maritime transportation that are sustainable and which have lower greenhouse gas emissions. Methanol is one such alternative fuel that has garnered considerable attention given its potential to be produced by more sustainable processes and its more favorable greenhouse gas emission profile in comparison with current fossil fuels. Understanding the physical and chemical properties of methanol under a range of conditions is essential for its development as a marine fuel. In this study, we seek to define physical and chemical properties of different methanol samples to simulate real-world storage conditions as these data are lacking in the literature. Several methanol samples were evaluated: nearly pure methanol; International Organization for Standardization (ISO) marine methanol (MM) grades A, B, and C; and methanol plus higher alcohols. We first evaluated all methanol samples for impurities, acetic acid content, density, and distillation range. We then characterized the effects of water absorption and found that methanol can easily absorb unacceptable water content from humid air within hours, necessitating storage conditions that prevent this process. In eight-week aging experiments at 20 °C and 40 °C in ambient air, we did not observe significant oxidation for any of the methanol samples; however, we did observe increases in acid number. We assessed the impact of contamination of methanol with water, marine gas oil (MGO), and an MGO–biodiesel mixture on density, viscosity, distillation range, and lubricity. Finally, we show that MGO contamination of methanol results in a slight increase in sooting tendency. In aggregate, our results provide an in-depth analysis of physical and chemical properties of methanol as well as the impacts of storage conditions and impurities on the properties of fuel methanol.

09 BIOMASS FUELS↗
DOE OSTI2026

The DECam MAGIC Survey $-$ Mapping the Ancient Galaxy in CaHK: Overview and Summary of Early Science

We present the DECam Mapping the Ancient Galaxy in CaHK (MAGIC) survey, a 54-night NOIRLab Survey Program to image $\gtrsim$5,000$\,$deg$^2$ of the southern hemisphere using a metallicity-sensitive narrow-band filter covering the Ca$\,$ii$\,$H&K lines centered at 3955$\,$A. This filter is installed on the Dark Energy Camera (DECam), mounted on the 4-m NSF Víctor M. Blanco Telescope. The survey reaches typical $10σ$ depths of $\text{mag}_{\text{CaHK}} \approx 22.5$, 3$-$4$\,$mag deeper than comparable surveys in the southern hemisphere. By combining photometry from this Ca$\,$ii$\,$H&K filter with existing DECam $g,r,i$ broadband photometry from the DECam Local Volume Exploration (DELVE) survey, MAGIC is deriving photometric metallicities for red giant branch stars down to the magnitude limit of usable proper motions from Gaia data release 3 (DR3). MAGIC has already imaged $\sim$3,000$\,$deg$^2$, supplemented by other affiliated observing programs that have used this filter to image star clusters, dwarf galaxies, and stellar streams. We overview MAGIC's survey strategy, describe data processing through the derivation of metallicities and photometric distances, and summarize early science results that have been published with this dataset. In addition, we present several new results, including the confirmation of a distant ($>5\,r_h$) member of the Reticulum II ultra-faint dwarf galaxy, on-sky density maps of low-metallicity stars into the distant Milky Way halo ($\sim150\,$kpc) recovering 13/14 ultra-faint dwarf galaxies in the current footprint, and a validation of our initial targeting of extremely metal-poor stars. Collectively, these results demonstrate that the MAGIC dataset enables cutting-edge studies of the faint, low-metallicity regime of the Milky Way and its substructures.

Chiti, A. [KIPAC, Menlo Park] (ORCID:0000000271556↗