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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Wolffia, a minimalist plant and synthetic biology chassis

A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Finally, systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The incongruity of validating quantitative proteomics using western blots

Similar to the age-old reviewer request for quantitative PCR validation of RNA sequencing data, nearly every researcher using proteomics technologies has, at one time or another, been asked by a reviewer to provide “western blot validation” of their mass spectrometry-based protein abundance data. We believe this request demonstrates a lack of awareness amongst the plant biology community about the extraordinary improvements in cost, sensitivity and reliability the field of mass spectrometry-based proteomics has made in recent years. Here, in this study, as a group of experts in different domains of quantitative plant proteomics, we explain why “western blot validation” of quantitative proteomics data is both unnecessary and invalid. Furthermore, we invite our colleagues in the plant science community to update their perception of quantitative mass spectrometry as a sensitive and reliable method of protein identification and quantitation.

Mehta, Devang↗
DOE OSTI2025

Review: Recent advances of ToF-SIMS for environmental analysis and imaging

Background: Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface analysis technique, initially developed and applied in inorganic materials and semiconductors. In past decades, ToF-SIMS has attracted more attention in its analysis capabilities of organic materials, with increased applications in biology, medical, and health development. It has also become a versatile and effective tool in environmental analysis due to its high mass resolution, mass accuracy, and depth profiling. Results: In this review, we first give an overview of the principle of ToF-SIMS and follow with recent ToF-SIMS applications in exemplary environmental study cases, including atmospheric aerosol, soil, water, plant, and organic solvent analysis. Moreover, sample preparation techniques are summarized in relation to corresponding environmental applications. Specifically, we call attention to ToF-SIMS investigations showcasing studies in surface chemical compositions, images, and depth profile analysis. These findings emphasize the important role of interfacial chemistry in environmental processes and provide valuable insights into dynamic processes, such as chemical transformation, particle formation, plant biology, and microbial inspired biotechnology development. The mass spectral imaging results acquired by ToF-SIMS offer a deeper understanding of intermediate stages and transient phases for environmental specimens. Significance: In situ and operando imaging offer new possibilities in studying phenomena in real time with high spatial resolution. Furthermore, it is anticipated that more research groups will use ToF-SIMS in environmental research given recent advances in measurement capabilities and surging needs in chemical mapping of complex analytes and systems.

Aerosol↗
DOE OSTI2022

Rays for Roots - Integrating Backscatter X-Ray Phenotyping, Modeling and Genetics to Increase Carbon Sequestration and Switchgrass Resource Use (Final Report)

To increase carbon (C) deposition in the soil and enhance crop resource use efficiency, characterizing root form and function is essential. Several root and soil traits have been linked to increased root-to-soil C transfer. Technology that could provide high-resolution characterization of many of these traits in field conditions would revolutionize our ability to study and understand how to increase C sequestration. In this effort, we developed an initial early prototype backscatter X-ray system for non-destructive imaging of root traits. We collected initial backscatter X-ray data in field and lab settings and carried out early analysis of these data. Along with this prototype, we also developed a suite of root phenotyping approaches including advanced minirhizotron image analysis, soil core imaging, and mesocosm imaging. Minirhizotron (MR) tubes are clear tubes inserted into the soil in the field and used to image roots and the surrounding soil. Our team has developed deep learning-based methods that can segment roots from soil that can learn from imprecise image-level labels. The ability to learn or fine-tune our deep learning algorithms from image-level labels allows easier and faster application of these approaches to new locations and new plant species. We have successfully implemented and applied our MR analysis approaches to thousands of switchgrass MR images collected across geographical regions. An advantage of MR imaging is the ability to collect root and soil images over time. Our soil core analysis included collecting hundreds of soil core samples from harvested switchgrass fields and imaging these cores with both X-ray CT and backscatter X-ray imaging. Initial segmentation approaches for the X-ray CT images of these cores have been developed and applied. An advantage of soil core analysis is that it preserves the three-dimensional structures of the roots and soil in the core collected. Our group also developed photogrammetry-based mesocosm root imaging and phenotyping approaches. In this approach, a plant was grown in a large mesocosm with a three-dimensional grid of thin supporting lines inserted throughout the mesocosm. After the plant (and, correspondingly, the root architecture is grown and established) the soil media was removed and the supporting lines approximately preserved the three-dimensional root architecture. Then, we applied photogrammetry techniques to create a three-dimensional digital representation of the root architecture for which we developed analysis algorithms including skeletonization. We carried out our phenotyping development with powerful switchgrass resources and physiological and agroecosystem modeling to deliver novel technology. This project contributes to multiple ARPA-E missions including reduction of foreign imports of energy, reduction of energy-related emissions including greenhouse gases, and ensuring that the United States maintains a technological lead in developing and deploying advanced energy technology. Furthermore, the developed tools could transform public and private plant breeding and could be broadly applicable to other crops and, potentially, other application areas. Our team of engineers, plant and soil scientists, and modelers i) developed an early prototype backscatter X-ray platform that can operate in field conditions; ii) developed a suite of root phenotyping and characterization approaches as described above; iii) developed and carried out plant biology and physiology roots studies and; iv) developed and implemented mechanistic physiological modeling.

42 ENGINEERING↗
DOE OSTI2023

Overcoming the field-of-view to diameter trade-off in microendoscopy via computational optrode-array microscopy

High-resolution microscopy of deep tissue with large field-of-view (FOV) is critical for elucidating organization of cellular structures in plant biology. Microscopy with an implanted probe offers an effective solution. However, there exists a fundamental trade-off between the FOV and probe diameter arising from aberrations inherent in conventional imaging optics (typically, FOV < 30% of diameter). Here, we demonstrate the use of microfabricated non-imaging probes (optrodes) that when combined with a trained machine-learning algorithm is able to achieve FOV of 1x to 5x the probe diameter. Further increase in FOV is achieved by using multiple optrodes in parallel. With a 1 × 2 optrode array, we demonstrate imaging of fluorescent beads (including 30 FPS video), stained plant stem sections and stained living stems. Our demonstration lays the foundation for fast, high-resolution microscopy with large FOV in deep tissue via microfabricated non-imaging probes and advanced machine learning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

Cell signaling↗
DOE OSTI2025

Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high-magnification, complex microscopy images, such as those generated by freeze-fracture electron microscopy (FF-TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high-throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF-TEM images. The pipeline integrates preprocessing, detection, human-in-the-loop verification, and semantic segmentation to quantify features such as rosette diameter and inter-lobe spacing. The approach was trained and tested on a curated dataset of high-resolution FF-TEM micrographs of Physcomitrium patens, expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50-95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high-throughput applications. Our results show that the pipeline achieves human-expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)-assisted workflows in biological imaging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ectopic expression of pectate lyase PtxtPL1-27 in aspen affects leaf cuticle development

Cuticle - a hydrophobic barrier of cutin and waxes covering the outer cell wall surface of plants - enables survival in terrestrial habitats. However, it is not understood how the hydrophobic cuticle precursors travel through the homogalacturonan-rich hydrophilic cell wall. To elucidate the role of homogalacturonan in cuticle development, we disrupted its integrity by overexpressing a pectate lyase, PtxtPL1-27, in aspen. PtxtPL1-27 had pleiotropic effects on shoot development, including the reduction of cuticle thickness and changes in cutin and wax composition, but the expression of cutin biosynthetic genes was little affected. Despite a reduction in homogalacturonan content in the leaves, labeling with the homogalacturonan-specific antibody JIM5 in the outer epidermal cell wall layer increased and displayed an altered pattern. Moreover, the ultrastructure of cell walls was changed concomitant with lipid accumulation. We propose that the disruption of homogalacturonan integrity affected the cutinsome-dependent transport and polymerization of cutin monomers in the cell wall.

Plant Biology↗
DOE OSTI2025

Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-dependent synergy and antagonism

Agrobacterium pathogenesis, which involves transferring T-DNA into plant cells, is the cornerstone of plant genetic engineering. As the applications that rely on Agrobacterium increase in sophistication, it becomes critical to achieve a quantitative and predictive understanding of T-DNA expression at the level of single plant cells. Here we examine if a classic Poisson model of interactions between pathogens and host cells holds true for Agrobacterium infecting Nicotiana benthamiana. Systematically challenging this model revealed antagonistic and synergistic density-dependent interactions between bacteria that do not require quorum sensing. Using various approaches, we studied the molecular basis of these interactions. To overcome the engineering constraints imposed by antagonism, we created a dual binary vector system termed ‘BiBi’, which can improve the efficiency of a reconstituted complex metabolic pathway in a predictive fashion. Our findings illustrate how combining theoretical models with quantitative experiments can reveal new principles of bacterial pathogenesis, impacting both fundamental and applied plant biology.

Alamos, Simon↗
DOE OSTI2025

Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield

Switchgrass (Panicum virgatum) is a promising bioenergy crop due in part to its resilience to drought stress. However, the significance of drought timing remains poorly understood, both from a plant biology perspective and its impact on downstream biofuel production. This study determines the developmental stage-specific physiological and metabolic responses of switchgrass to drought stress and its implications for biofuel production using a custom-built programmable irrigation system. Vegetative, flowering, and senescence-stage drought significantly reduced carbon dioxide assimilation, and stomatal conductance without affecting biomass yield. Metabolic profiling revealed significant accumulation of glucose, fructose, quinic acid, shikimate and GABA during vegetative-stage drought, while flowering and senescence stages exhibited limited metabolic changes. Similarly, specialized metabolites also displayed distinct developmental patterns, with vegetative-stage drought driving the most pronounced metabolic alterations. Thermochemically-treated and hydrolyzed switchgrass biomass from vegetative-stage drought showed elevated lignocellulose-derived compounds and saponins with the latter most positively correlating with fermentation lag times. Conversely, senescence-stage drought enhanced ethanol yields while lowering saponin levels in the hydrolysates. While vegetative-stage drought enhanced physiological resilience, it compromises downstream biofuel production by introducing fermentation inhibitors, particularly saponins.

biofuel↗
DOE OSTI2023

Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

Abstract Life on Earth depends on the conversion of solar energy to chemical energy by plants through photosynthesis. A fundamental challenge in optimizing photosynthesis is to adjust leaf angles to efficiently use the intercepted sunlight under the constraints of heat stress, water loss and competition. Despite the importance of leaf angle, until recently, we have lacked data and frameworks to describe and predict leaf angle dynamics and their impacts on leaves to the globe. We review the role of leaf angle in studies of ecophysiology, ecosystem ecology and earth system science, and highlight the essential yet understudied role of leaf angle as an ecological strategy to regulate plant carbon–water–energy nexus and to bridge leaf, canopy and earth system processes. Using two models, we show that leaf angle variations have significant impacts on not only canopy‐scale photosynthesis, energy balance and water use efficiency but also light competition within the forest canopy. New techniques to measure leaf angles are emerging, opening opportunities to understand the rarely‐measured intraspecific, interspecific, seasonal and interannual variations of leaf angles and their implications to plant biology and earth system science. We conclude by proposing three directions for future research.

Yang, Xi↗
DOE OSTI2022

Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait

Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. Here, we examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm 2 yr –1 ) that genotypes invest in, they lose 1.2 to 1.7 units (mg g –1 NSC) of storage. Across species, for each additional unit of area growth (in cm 2 yr –1 ), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes

SUMMARY Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum , a drought and heat‐tolerant C4 species, requires a vast, large‐scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large‐scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)‐induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis ‐regulatory elements. A comparison of the distribution of mutations in the large‐scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS‐induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5′ UTR, gene body, and 3′‐UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the K a / K s value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB ( https://www.depts.ttu.edu/igcast/sorbmutdb.php ) and SorghumBase ( https://sorghumbase.org/ ). This current large‐scale sequence‐indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

cis -Regulatory Elements in Plant Development, Adaptation, and Evolution

cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Ornamental origins and genomic frontiers: a review of big-bracted dogwood research

The big-bracted (Benthamidia) dogwood clade consists of small- to medium-sized deciduous trees within the genus Cornus, known for their showy spring-time floral bract display. Cornus is within the family Cornaceae and order Cornales, and as Cornales is one of the earliest diverging asterids, these taxa have been important for phylogenetic research. Three species within the big-bracted clade, flowering (Cornus florida), kousa (C. kousa), and Pacific (C. nuttallii) dogwoods, are popular ornamental landscape plants in North America, with more than 130 cultivars released. Despite their commercial popularity, numerous research gaps have limited the expansion of fundamental research and dogwood breeding programs. In this present review, we aim to provide a thorough overview of our current understanding of 1) the phylogenetic and biogeographic context, 2) plant biology and major pests and pathogens impacting commercialization, 3) historical commercialization and propagation methods, and 4) genetic and genomic resources and how they have been implemented to understand these species. Research gaps and future directions to advance basic research and breeding of big-bracted ornamental dogwoods are discussed throughout.

Cornus florida↗
DOE OSTI2021

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions

Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.

dissolved oxygen↗
DOE OSTI2026

26th International Symposium on Plant Lipids

The 2024 International Symposium on Plant Lipids (ISPL) successfully advanced scientific knowledge in plant lipid biology by presenting new discoveries in lipid metabolism, membrane structure and function, lipid signaling, and biotechnology. The symposium fostered professional development for early-career scientists through oral and poster presentation opportunities, lightning talks, and networking events. It promoted the exchange of new technologies, including advances in mass spectrometry, metabolic modeling, and synthetic biology, that will accelerate research across plant biology and related fields. ISPL also strengthened international collaborations, drawing 220 participants from 15 countries across four continents, and established a platform for ongoing scientific exchange and community-building within the global plant lipid research community.

59 BASIC BIOLOGICAL SCIENCES↗