Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “EMBRYO”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

16 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Twin nucleation and growth in hexagonal close-packed metals: The role of slip-mediated plasticity on twin embryo formation and evolution

Twinning is a key deformation mechanism in hexagonal close-packed (hcp) metals, which are typified by a lack of easily activated slip systems that can accommodate a general state of loading. Pragmatically, the nucleation and evolution of twin domains occurs concomitantly with slip, such that the eventual twin network is conditioned by both external and internal stresses resulting, among others, from the evolution of dislocations. However our understanding of the interplay between dislocations, and twin nucleation and stability remains limited. This work focuses on elucidating the influence of dislocation-mediated plasticity on the formation, growth, and stability of twin embryos. First, a new mesoscale spectral crystal plasticity-twinning framework is developed and used to quantify the change in the free energy landscape following the nucleation {$10\bar{1}2$} of twins in Mg. Representative twin morphologies are modeled under conditions of limited and profuse slip activity, which are emulative of small- and bulk-scale samples, respectively. Then, the driving traction profiles around twin embryos are investigated via a sharp interface approach to obtain insights into how concurrent slip-mediated plasticity can influence the growth/stabilization of nanometric twins. The driving traction profiles are further utilized to determine the stability of twin embryos post loading. The initial dislocation density in the samples, and within the different domains (i.e., twin vs. parent), is seen to have a significant effect on the twin nucleation stress. Namely, the activation of high levels of concomitant plasticity in the parent grain is seen to significantly drive the formation of nanometric twin nuclei at stresses as low as 250 MPa. Further, the sharp interface analysis reveals that profuse plasticity in the parent grain simultaneously alters the forward and back stresses, such that the magnitude/polarity of the driving tractions become increasingly favorable for nanometric twin growth when slip is active. Finally, prior plasticity in the parent grain is seen to result in favorable driving tractions for nanometric twin growth, even at applied stresses as low as ~ 100 MPa. In conclusion, these results are in stark contrast to a case without any dislocations, wherein applied stresses as high as ~ 500 MPa are necessary to grow the twin domains.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development

Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsis thaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence of these elements on expression patterns is already exerted during embryogenesis and functional in the context of the early embryo. Finally, we reveal the existence of a BOX-mediated autoregulatory feedback loop that, in large part, explains CNS influence on expression patterns. We thus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.

PLETHORA↗
DOE OSTI2024

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

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

McGuire, Sean T.↗
DOE OSTI2025

Impact of developmental methylmercury exposure on avian embryonic development, hatchling growth, and survival

Abstract Methylmercury (MeHg) is a globally ubiquitous and persistent environmental toxicant that negatively affects animal behavior, health, and reproduction. In birds, MeHg is transferred from female to egg, contaminating embryos during sensitive stages of early embryonic development and growth. This toxic exposure in the prenatal environment not only induces mortality but also possible lasting impacts on physiology, health, and survival, even once hatched. The purpose of our study was to further elucidate the negative effects of MeHg exposure during avian embryonic development and explore how such exposure can impact offspring development, growth, and survival, both in ovo and posthatch. To assess this, we experimentally dosed fertile mallard and wood duck eggs with MeHg II chloride and reared developing embryos and ducklings to various endpoints. We found that embryos not only readily accumulated MeHg throughout incubation, but they also displayed varying dose-dependent disparities in body mass and morphometrics, with control individuals being larger during early and late embryonic stages of development (p < 0.05). Furthermore, hatched offspring exposed to MeHg exhibited increasingly slower growth rates between 7 to 10 and 10 to 15 days posthatch (p < 0.05), and were found to have lower survival probabilities both under controlled laboratory conditions (p < 0.005), and in the natural environment (p < 0.05). Our findings on the detrimental effects of MeHg on avian embryos and hatchlings emphasize the need for more proactive means of environmental protection and remediation to protect vulnerable avian populations and the ecosystems they inhabit.

Leaphart, James C.↗
DOE OSTI2026

Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil

Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed 13 C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. Here, in cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid–protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigation of the Sensitivity of Tropical Cyclogenesis to Aerosol Intervention

Abstract As risks from tropical cyclones (TCs) are fueled by climate change escalation, there is an urgent need for transformational solutions to complement traditional approaches. Seeding TCs using aerosols can be a promising method to reduce cyclone intensity, supported by theoretical understanding of the microphysical effects of aerosols on TC clouds. The ideal time to intervene effectively in TCs is likely during their initial stage, before TC wind speeds reach their peak. However, studies exploring potential aerosol effects on TC formation remain scarce. This study investigates how a TC embryo responds to the addition of aerosols of varying sizes using the Weather Research & Forecasting (WRF) model coupled with a spectral‐bin microphysics model. We found that aerosols of different sizes and concentrations distinctively affect the pre‐TC vortex's microstructure and dynamics. Fine and ultrafine aerosols enhance the latent heat of condensation, freezing, deposition, and riming, initially intensifying the vortex. However, this results in enhancement of the cold pool, thereby reducing inflow and surface fluxes, subsequently weakening the vortex. Coarse aerosols produce the opposite effect to that of fine and ultrafine aerosols. Coarse aerosols lead to a slower initial acceleration owing to enhanced warm rain. However, the resulting weaker cold pool is insufficient to effectively reduce the strength of the vortex at the later stage. This study provides critical insights into how aerosols of varying sizes and concentrations modulate the energy cascade and impact the evolution of a TC embryo, laying the groundwork for further research on TC risk management through aerosol intervention.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Dampening of the Precipitation Response to Aerosol Pollution From Turbulence in Cumulus Clouds

Using aircraft observations and a cloud model with particle‐based microphysics, it is shown that the enhancement of drop collision‐coalescence from turbulence in clouds not only leads to earlier onset of rain in warm cumulus clouds as past studies have suggested, but also significantly dampens the precipitation susceptibility to aerosol loading. Enhanced drop coalescence from turbulence substantially increases the production of drizzle embryos just above cloud base, which in turn act as seeds that accelerate rain drop growth at mid and upper cloud levels even in highly polluted conditions. In contrast, pollution aerosols strongly inhibit rainfall when the commonly assumed gravitational‐only collision kernel is used and turbulent coalescence is neglected. Overall, turbulence‐enhanced drop coalescence strongly influences the response of warm cumulus clouds and precipitation to aerosol loading, suggesting that the effects of turbulent coalescence should be included in Earth system model representations of aerosol‐cloud‐precipitation interactions and aerosol indirect radiative forcing.

Chandrakar, Kamal Kant [NSF National Center for At↗
DOE OSTI2025

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity

High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.

Kosicki, Michael↗
DOE OSTI2025

Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOViFT (adaptive optical vision Fourier transformer)—a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Alshaabi, Thayer [Howard Hughes Medical Institute,↗
DOE OSTI2025

Completion of lunar magma ocean solidification at 4.43 Ga

Crystallization of the lunar magma ocean yielded a chemically unique liquid residuum named KREEP. This component is expressed as a large patch on the near side of the Moon and a possible smaller patch in the northwest portion of the Moon’s South Pole-Aitken basin on the far side. Thermal models estimate that the crystallization of the lunar magma ocean (LMO) could have spanned from 10 and 200 My, while studies of radioactive decay systems have yielded inconsistent ages for the completion of LMO crystallization covering over 160 My. Here, we show that the Moon achieved >99% crystallization at 4,429 ± 76 Ma, indicating a lunar formation age of ~4,450 Ma or possibly older. Using the 176 Lu– 176 Hf decay system (t 1/2 = 37 Gy), we found that the initial 176 Hf/ 177 Hf ratios of lunar zircons with varied U–Pb ages are consistent with their crystallization from a KREEP-rich reservoir with a consistently low 176 Lu/ 177 Hf ratio of 0.0167 that emerged ~140 My after solar system formation. The previously proposed younger model age of ~4.33 Ga for the source of mare basalts (240 My after solar system formation) might reflect the timing of a large impact. Our results demonstrate that lunar magma ocean crystallization took place while the Moon was still battered by planetary embryos and planetesimals leftover from the main stage of planetary accretion. The study of Lu–Hf model ages for samples brought back from the South Pole-Aitken basin will help to assess the lateral continuity of KREEP and further understand its significance in the early history of the Moon.

Science & Technology - Other Topics↗
DOE OSTI2025

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗
DOE OSTI2024

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Propelling sustainable energy: Multi-omics analysis of pennycress FATTY ACID ELONGATION1 knockout for biofuel production

Abstract The aviation industry’s growing interest in renewable jet fuel has encouraged the exploration of alternative oilseed crops. Replacing traditional fossil fuels with a sustainable, domestically sourced crop can substantially reduce carbon emissions, thus mitigating global climate instability. Pennycress (Thlaspi arvense L.) is an emerging oilseed intermediate crop that can be grown during the offseason between maize (Zea mays) and soybean (Glycine max) to produce renewable biofuel. Pennycress is being domesticated through breeding and mutagenesis, providing opportunities for trait enhancement. Here, we employed metabolic engineering strategies to improve seed oil composition and bolster the plant's economic competitiveness. FATTY ACID ELONGATION1 (FAE1) was targeted using CRISPR-Cas 9 gene editing to eliminate very long chain fatty acids (VLCFAs) from pennycress seed oil, thereby enhancing its cold flow properties. Through an integrated multiomics approach, we investigated the impact of eliminating VLCFAs in developing and mature plant embryos. Our findings revealed improved cold-germination efficiency in fae1, with seedling emergence occurring up to 3 d earlier at 10 °C. However, these alterations led to a tradeoff between storage oil content and composition. Additionally, these shifts in lipid biosynthesis were accompanied by broad metabolic changes, such as the accumulation of glucose and ADP-glucose quantities consistent with increased starch production. Furthermore, shifts to shorter FA chains triggered the upregulation of heat shock proteins, underscoring the importance of VLCFAs in stress signaling pathways. Overall, this research provides crucial insights for optimizing pennycress seed oil while preserving essential traits for biofuel applications.

Rasoul, Amira (ORCID:0009000714290175)↗
DOE OSTI2025

Thermal and mechanical influences on shear band formation and suppression in shocked 1,3,5-trinitroperhydro-1,3,5-triazine (RDX)

High-pressure shear band formation is a critical phenomenon in energetic materials because of its ability to form hotspots and influence mechanical strength. Shear banding is known to occur in a variety of these materials, but the governing dynamics of the mechanisms are not well defined for molecular crystals. Our previous work has found that at high pressures in 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), the initial formation sites for shear bands, called “embryos”, form in excess and rapidly lower deviatoric stresses prior to shear band formation and growth, suppressing the shear banding nucleation and growth. Here, in this work, we assess the influence of a variety of changes to the material state on this phenomenon, including altered initial temperature, lateral strain that confines the system in tension or pressure, and initial molecular vacancies throughout the crystal. Shear band suppression and the nature of the shear band network are assessed as a function of each of these.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Advancing stem cell technologies for conservation of wildlife biodiversity

ABSTRACT Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Developmental Biology↗
DOE OSTI2025

Woody Plant Transformation: Current Status, Challenges, and Future Perspectives

Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future.

Agrobacterium tumefaciens↗