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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Visibility and annoyance of the phantom array effect varies with age and history of migraine

The phantom array effect (PAE) is a series of repeated images that may be perceived when a person moves their eyes in large saccades across a light source (or a specular reflection of that light source) that is modulating in output over time. Fifty-five people, including a group of 25 who experience migraine, evaluated the visibility and annoyingness of phantom arrays produced by 85 unique temporal light modulation waveforms (including sine, rectangular, complex and DC waveforms) generated using an LED placed against a black background. Those with migraine exhibited higher average visibility compared to those without migraine ( p = 0.019) and were relatively more sensitive at higher frequencies ( p < 0.001). Younger participants also found more stimuli to be visible ( p < 0.001). The threshold sensitivity function was similar to that developed for the phantom array visibility measure (PAVM), and PAVM was effective in predicting visibility ( R 2 = 0.87 for the relevant region of PAVM < 3). While those in the migraine group did not report seeing the PAE more often in everyday life at a statistically significant level, they reported being more annoyed by it and having more unwanted physiological responses (headaches, eye fatigue and distraction/disorientation). Members of the migraine group were also more likely to have changed their behaviour in architectural spaces (such as leaving a restaurant with ‘flickering’ lights). In the four hours after completing the experiment, 64% of the migraine group (vs. 19% of the non-migraine group) reported experiencing discomfort or an adverse reaction. In particular, 41% reported experiencing a headache (vs. 8% for those in the non-migraine group).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering

Microbial biotechnologies are key to addressing grand challenges to promote human health, reverse carbon emissions, recycle mixed plastic waste, remediate contaminated soils, and achieve sustainable economies. Synthetic biology has enabled design of diverse microbes and their proteins for useful purposes, but the narrowness of the natural genetic code limits functional diversity (e.g., biosynthesis) of engineered microbes. The natural genetic code defines the fundamental rules of translating genetic information into proteins comprised of 22 ‘canonical’ amino acids. However, using a technique called genetic code expansion (GCE), the chemical properties and therefore functions of proteins can be transformed by incorporation of one or more of ~200 chemically diverse ‘non-canonical’ amino acids. The effective application of genetic code expansion in diverse microbes has the potential to revolutionize biotechnology. However, despite over 50 years of research and its transformative potential, the application of genetic code expansion has been limited to a handful of bacterial species. In this project, we will perform three tasks to both overcome the barriers that prevent wide spread adoption of GCE as molecular tool and demonstrate its potential for biotechnological applications. Specifically, we will (1) develop a genetic engineering methodology that will enable use of GCE in a broad range of bacterial hosts, (2) use high-throughput functional genomics methods to identify physiological responses to both genetic code expansion and exposure to non-canonical amino acids in three different bacteria, and (3) demonstrate an application of GCE by selectively incorporate non-canonical amino acids into surface displayed peptides such as those used for biomining.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Morpho-physiological and transcriptomic responses of field pennycress to waterlogging

Field pennycress (Thlaspi arvense) is a new biofuel winter annual crop with extreme cold hardiness and a short life cycle, enabling off-season integration into corn and soybean rotations across the U.S. Midwest. Pennycress fields are susceptible to winter snow melt and spring rainfall, leading to waterlogged soils. The objective of this research was to determine the extent to which waterlogging during the reproductive stage affected gene expression, morphology, physiology, recovery, and yield between two pennycress lines (SP32-10 and MN106). In a controlled environment, total pod number, shoot/root dry weight, and total seed count/weight were significantly reduced in SP32-10 in response to waterlogging, whereas primary branch number, shoot dry weight, and single seed weight were significantly reduced in MN106. This indicated waterlogging had a greater negative impact on seed yield in SP32-10 than MN106. We compared the transcriptomic response of SP32-10 and MN106 to determine the gene expression patterns underlying these different responses to seven days of waterlogging. The number of differentially expressed genes (DEGs) between waterlogged and control roots were doubled in MN106 (3,424) compared to SP32-10 (1,767). Functional enrichment analysis of upregulated DEGs revealed Gene Ontology (GO) terms associated with hypoxia and decreased oxygen, with genes in these categories encoding proteins involved in alcoholic fermentation and glycolysis. Additionally, downregulated DEGs revealed GO terms associated with cell wall biogenesis and suberin biosynthesis, indicating suppressed growth and energy conservation. Interestingly, MN106 waterlogged roots exhibited significant stronger regulation of these genes than SP32-10, displaying a more robust transcriptomic response overall. Together, these results reveal the reconfiguration of cellular and metabolic processes in response to the severe energy crisis invoked by waterlogging in pennycress.

ERF-VII↗
DOE OSTI2026

Connecting agriculture and renewable energy: insights into microclimatic changes, physiological, biochemical, and yield responses under agrivoltaics: a review

Agrivoltaics, the synergistic integration of agriculture and solar energy production on the same piece of land, has emerged as a compelling dual-use solution that maximizes land productivity while simultaneously addressing the need for sustainable agricultural practices and renewable energy generation. Despite the growing global interest in this dual-use system, the microclimatic shifts created beneath solar panels and their consequences for crop performance remain insufficiently synthesized. This review highlights the intricate interactions between agrivoltaics systems and plant microclimates, discussing their impacts on various physiological processes, metabolic pathways, and overall yield responses in different crop species. Evidence indicates that moderated light intensity and altered microclimates can enhance water-use efficiency, stabilize photosynthetic function, and trigger beneficial metabolic adjustments; however, responses remain highly species-specific and strongly dependent on regional climate conditions and panel configuration. Yield outcomes vary widely among vegetables, cereals, pulses, and fruit crops, highlighting the necessity for tailored agronomic strategies and crop selection within agrivoltaic designs. A critical knowledge gap identified in this review concerns the limited understanding of molecular and omics-level responses underlying plant adaptation to agrivoltaic environments. We further provide a detailed and interdisciplinary overview of adaptive agronomic strategies, and optimal crop selection, tailored to agrivoltaic systems. Despite the benefits of land use efficiency and simultaneous food and energy production, challenges remain concerning initial investment, technological adaptation, social and legal barriers, and shade-induced yield penalties. Further research in this area will be critical to enhancing the agricultural, environmental, and economic sustainability of agrivoltaics while simultaneously augmenting their practical utility and appeal to farmers in the future.

14 SOLAR ENERGY↗
DOE OSTI2025

Intracellular Biomacromolecule Delivery by Stimuli-Responsive Protein Vesicles Loaded by Hydrophobic Ion Pairing

Proteins can perform ideal therapeutic functions. However, their large size and significant surface hydrophilicity and charge prohibit them from reaching intracellular targets. These chemical features also render them poorly encapsulated by nanoparticles used for intracellular delivery. In this work, a novel combination of protein vesicles and hydrophobic ion pairing (HIP) was used to load protein cargo and achieve cytosolic delivery to overcome the limitations of previous protein vesicle properties. Protein vesicles are thermally self-assembling nanoparticles made from elastin-like polypeptide (ELP) fused to an arginine-rich leucine zipper and a globular protein fused to a glutamate-rich leucine zipper. To impart stimuli-responsive disassembly, physiological stability, and small size, the ELP sequence was modified to include histidine and tyrosine residues. HIP was used to load and release protein cargo requiring endosomal escape for cytosolic function. HIP vesicles enabled delivery of cytochrome c, a cytosolically active protein, and a significant reduction in viability in both a traditional two-dimensional (2D) human cancer cell line culture and a biomimetic three-dimensional (3D) organoid model of acute myeloid leukemia. By examining the uptake of positively and negatively charged fluorescent protein cargos loaded by HIP, this work revealed the necessity of HIP for cytosolic cargo delivery and how HIP loading influences protein vesicle self-assembly and disassembly using microscopy, small-angle X-ray scattering, and nanoparticle tracking analysis. HIP protein vesicles have the potential to broaden the use of intracellular proteins as therapeutics for various diseases and extend protein vesicles to deliver other biomacromolecules, as the strategy developed here resulted in the first cytosolic protein cargo delivery using protein vesicles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

2024 IUFRO Tree Biotechnology Conference (Aug 4-8, 2024)

The 2024 IUFRO Tree Biotechnology Conference is the biennial meeting on genomics, molecular biology, and biotechnology of forest trees, associated with the IUFRO Working Party 2.04.06. This year's meeting was held in Annapolis, MD, USA from August 4th to 8th and was hosted by Yiping Qi (University of Maryland), Edward Eisenstein (University of Maryland), Gary Coleman (University of Maryland), and Heather Coleman (Syracuse University). The conference covered seven topics over the course of five days: 1) Biological and ecological insights from OMICS, 2) Advancing technologies for targeted trait manipulation and acceptability to diverse tree species, 3) Genes, development, and physiology, 4) Translating genomics and biotechnology to practice, 5) Trees in a changing world, 6) Genetic and phenotypic diversity for breeding and genomic selection, and 7) Biotechnology for biomaterials and bioeconomy. In addition to the sessions, there were two plenary sessions, provided by John Ralph (University of Wisconsin) and Tanja Pyrhäjärvi (University of Helsinki). The meeting celebrated the second awardees of the newly created IUFRO WG 2.04.06 Award: Excellence in Forest Molecular Biology and Genomics, which was presented to Chung-Jui (C.J.) Tsai (University of Georgia). Greg Goralogia (Oregon State University) was the recipient of the associated Early Career Award. The scientific presentations at the conference highlighted cutting-edge advancements in many facets of forest biotechnology research, including applications of genomic selection in forest genetics and breeding, the use of genetic editing, tree physiology, stress response, molecular breeding, wood development, "omics" technologies, and the social and economic impacts of genetically modified (GM) trees. Scientific take homes from the meeting include the power of NMR to dissect the composition of lignin, the genomic diversity of forest trees that has enormous potential for tree improvement and the integration of systems biology with climate and geographical data. The conference attracted a mix of students (25), postdoctoral fellows (32), and scientists from academia (66) and industry (18). In all, the conference was attended by 141 registered participants, representing 20 countries that participated in 23 invited lectures (including 6 'early-career' keynotes), 27 voluntary talks and 61 poster presentations. Support for the conference was drawn from a wide variety of Academia, Industry, and Government sources, and included financial support from several tree improvement companies. Overall, the conference was a great success, providing an exceptional mix of science and social activities in a relaxed and collegial atmosphere. More information about the meeting can be found at treebiotech.org. The next meeting will be held in Stellenbosch, South Africa, in 2026, hosted jointly by Zander Myburg, Dave Drew (University of Stellenbosch,) and Sanushka Naidoo (University of Pretoria, FABI).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A Review of Polymeric Nanoparticle Design, Synthesis, and Biomedical Applications

Polymeric nanoparticles (PNPs) are solid particles that contain macromolecular polymers ranging in size from 1-1000 nm. They have a wide variety of structures that are determined by their identity as either natural biopolymers, synthetic polymers or a combination of both. In the design of PNPs, the polymeric system, size, internal structure, additional molecules, and synthetic pathway can be engineered, allowing for a multitude of properties including differing responses to physiological environments and the incorporation of a drug. The easily accessible fine tuning of PNPs allows for a multitude of applications in medicine. PNPs allow for increased pharmacokinetics, efficacy, safety, and targeting strength when utilized as carriers for drugs. Currently there are a wide range of PNPs approved by the Food and Drug Administration for use in clinical settings and many more being investigated in clinical studies. There is also research that is being conducted for the usage of PNPs in controlled drug delivery systems and as carriers through the blood brain barrier to aid in treating neurological diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Normalized Solar-Induced Fluorescence Responds Earlier Than Vegetation Indices to the 2019 North China Plain Drought

Recently, solar-induced chlorophyll fluorescence (SIF) from satellites has shown potential for evaluating vegetation status and stress responses. Fluorescence quantum yield ($Φ_F$) is essentially linked to vegetation stress. However, the complex physiological and structural responses of SIF and $Φ_F$ to drought need further study. This study normalized SIF as SIFn to account for angular variations and fluctuations in photosynthetically active radiation (PAR), aiming for more accurate drought monitoring. SIFn anomalies were compared to historical baselines (2019–2021 averages) of vegetation indices (VIs), raw SIF, and $Φ_F$ during a 2019 drought in the North China Plain (NCP). Here, the results show SIFn provides an effective method for drought monitoring, showing the earliest decline compared to raw SIF, VIs, and $Φ_F$. In the first two weeks of drought, SIFn decreased by 8.2%, 7.0%, 12.5%, and 8.2% across the four NCP subdivisions. SIFn outperformed other indicators, proving sensitive to early drought detection. SIFn was also examined for tracking drought alleviation by rainfall. The uncertainty under different viewing geometries was quantified. SIFn anomalies showed a strong correlation with rainfall anomalies (R: 0.45 ~ 0.52) and meteorological factors like PAR (R: 0.80 ~ 0.84) and relative humidity (R:0.52 ~ 0.54). The correlation of near-infrared reflectance (NIRv) and $Φ_F$ anomalies with SIF was weak during drought onset (R: 0.16 ~ 0.32) but strong at the end (R: 0.83 ~ 0.87). These suggest both canopy structure (mainly characterized by NIRv) and vegetation chlorophyll ($Φ_F$) are impacted by drought and influence SIF at different stages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Abstract Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species–environment correlations to climatic conditions not currently experienced by a species, which can result in unrealistic predictions. For poikilotherms, incorporating species' thermal physiology to inform extrapolations under novel thermal conditions can result in more realistic predictions. Furthermore, models that incorporate species and spatial dependencies may improve predictions by capturing correlations present in ecological data that are not accounted for by predictor variables. Here, we present a joint species, spatially dependent physiologically guided abundance (jsPGA) model for predicting multispecies responses to climate warming. The jsPGA model uses a basis function approach to capture both species and spatial dependencies. We apply the jsPGA model to predict the response of eight fish species to projected climate warming in thousands of lakes in Minnesota, USA. By the end of the century, the cold‐adapted species was predicted to have high probabilities of extirpation across its current range—with 10% of lakes currently inhabited by this species having an extirpation probability >0.90. The remaining species had varying levels of predicted changes in abundance, reflecting differences in their thermal physiology. Though the model did not identify many strong species dependencies, the variation in estimated spatial dependence across species suggested that accounting for both dependencies was important for predicting the abundance of these fishes. The jsPGA model provides a new tool for predicting changes in the abundance, distribution, and extirpation probability of poikilotherms under novel thermal conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Permanent Stress Adaptation and Unexpected High Light Tolerance in the Shade-Adapted Chlamydomonas priscui

The Antarctic photopsychrophile, Chlamydomonas priscui UWO241, is adapted to extreme environmental conditions, including permanent low temperatures, high salt, and shade. During long-term exposure to this extreme habitat, UWO241 appears to have lost several short-term mechanisms in favor of constitutive protection against environmental stress. This study investigated the physiological and growth responses of UWO241 to high-light conditions, evaluating the impacts of long-term acclimation to high light, low temperature, and high salinity on its ability to manage short-term photoinhibition. We found that UWO241 significantly increased its growth rate and photosynthetic activity at growth irradiances far exceeding native light conditions. Furthermore, UWO241 exhibited robust protection against short-term photoinhibition, particularly in photosystem I. Lastly, pre-acclimation to high light or low temperatures, but not high salinity, enhanced photoinhibition tolerance. These findings extend our understanding of stress tolerance in extremophilic algae. In the past 2 decades, climate change-related increasing glacial stream flow has perturbed long-term stable conditions, which has been associated with lake level rise, the thinning of ice covers, and the expansion of ice-free perimeters, leading to perturbations in light and salinity conditions. Our findings have implications for phytoplankton survival and the response to change scenarios in the light-limited environment of Antarctic ice-covered lakes.

Plant Sciences↗
DOE OSTI2024

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana . Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Transcriptomic data sets examining several stress responses in Zymomonas mobilis strains

We used RNA-seq to compare gene expression from Zymomonas mobilis ZM4 grown under various conditions: aerobic ± paraquat, anaerobic ± hydrogen peroxide, or an iron chelator. We analyzed two mutant strains lacking predicted transcription factors (ZMO_0442 and ZMO_1411) grown under aerobic or anaerobic conditions. We report the RNA-seq data from these experiments.

Bacterial Stress Response↗