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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection

The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dynamic interactions at the mineral–organic matter interface

Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Insights from designing an artificial cascade catalysis system using principles from substrate channeling in enzymes

Generalizing the key requirements of highly-selective, multi-step chemical conversions involving spatially separated reaction centers remains one of the grand challenges of chemistry. Much work towards this effort has focused on decomposing multi-step conversions into their constituent reactions, whose intermediates are successively upgraded in a chemical cascade via diffusion from center to center. This approach for synthesizing more complex molecules takes its cues from biochemical networks, where near-unit conversion of even complex carbohydrates is achieved by upgrading chemical precursors via enzymatic cascades. In this computational study we examine a simple cascade involving coupled Ag and Cu catalysts that sequentially converts CO2 to CO and then CO2 and CO to reduced products, generically named CO2Product and COProduct. The system architecture is inspired by the phenomenon of biological substrate channeling, and components are examined to evaluate their effects on conversion efficiency in the cascade. Aside from a substrate channel linking two reaction centers, we find efficient cascades must also incorporate directional substrate diffusion, compartmentalization of the reaction centers, and proper timing of substrate arrival at the active center. We make explicit linkages between these requirements and chemical conversion in known biological systems, revealing additional control elements that could be incorporated.

CO 2 reduction↗
DOE OSTI2022

Membrane potential sensing: Material design and method development for single particle optical electrophysiology

We review the development of “single” nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for “non-genetic optogenetics.” The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (~2% Δλ spectral Stark shift up to ~30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining. Self-spiking- and patched-HEK293 cells and cortical neurons, when stained with hybrid nanobiomaterials, show clear photoluminescence intensity changes in response to membrane potential (MP) changes. Organic voltage nanosensors based on polystyrene beads and nanodisk technology utilize Fluorescence (Förster) Resonance Energy Transfer (FRET) to sense local electric fields. Voltage sensing FRET pairs achieve voltage sensitivity up to ~35% ΔF/F per 120 mV in cultures. Non-invasive MP recording from individual targeted sites (synapses and spines) with nanodisks has been realized. However, both of these QCSE- and FRET-based voltage nanosensors yet need to reach the milestone of recording individual action potentials from individual targeted sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Design of a robot-automated flat plate/reflection geometry x-ray diffraction setup for accelerated materials discovery and structural screening

Here, we report the design, construction, and automation of a flat plate sample loading, alignment, and data acquisition system for X-ray diffraction measurements in reflection geometry implemented at the Stanford Synchrotron Radiation Lightsource. The system is built onto a single platform, enabling facile transferability, and is compartmentalized into sample storage, sample transfer, and sample position/alignment segments. The core feature of this system is a six-axis robotic arm that offers a large range of highly reproducible and programable movements. The degrees of freedom of the robot arm enable adaptability in which movements can be modified to fit various beamline environments and sample configurations. Samples are housed on 3D printed sample mounts, which are arranged onto a 6 × 2 array of sample cassettes capable of holding 7 samples. Using sample mounts designed for solid oxide electrolysis button cells (SOECs), the maximum tray capacity is 84 samples, which can be aligned and run in ~ 24 hours with long exposure scans. The sample array is additionally capable of accommodating a range of sample sizes and geometries due to the rapid 3D printed fabrication. The components of the setup will be described in detail and performance will be demonstrated with a set of representative SOEC and XRD standard samples. Opportunities for future developments and integration with the automated setup are summarized.

08 HYDROGEN↗
DOE OSTI2025

Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution

Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to decouple. Here, we engineered synthetic intracellular antibodies (intrabodies) that are capable of modulating mTOR signaling with genetically programmable spatial resolution. Epitope-directed phage display was exploited to generate high affinity synthetic antibody fragments (Fabs) against the FKBP12–Rapamycin binding site of mTOR (mTOR FRB ). We determined high-resolution crystal structures of two unique Fabs that discriminate distinct conformational states of mTOR FRB through recognition of its substrate recruitment interface. By leveraging these conformation-specific binders as intracellular probes, we uncovered the structural basis for an allosteric mechanism governing mTOR complex 1 (mTORC1) stability mediated by subtle structural adjustments within mTOR FRB . Furthermore, our results demonstrated that synthetic binders emulate natural substrates by employing divergent yet complementary hydrophobic residues at defined positions, underscoring the broad molecular recognition capability of mTOR FRB . Intracellular signaling studies showed differential time-dependent inhibition of S6 kinase 1 and Akt phosphorylation by genetically encoded intrabodies, thus supporting a mechanism of inhibition analogous to the natural product rapamycin. Finally, we implemented a feasible approach to selectively modulate mTOR signaling in the nucleus through spatially programmed intrabody expression. These findings establish intrabodies as versatile tools for dissecting the conformational regulation of mTORC1 and should be useful to explore how location-specific mTOR signaling influences disease progression.

Science & Technology - Other Topics↗
DOE OSTI2023

Genomic Mysteries of Giant Bacteria: Insights and Implications

Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2–3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Permissiveness and competition within and between Neurospora crassa syncytia

A multinucleate syncytium is a common growth form in filamentous fungi. Comprehensive functions of the syncytial state remain unknown, but it likely allows for a wide range of adaptations to enable filamentous fungi to coordinate growth, reproduction, responses to the environment, and to distribute nuclear and cytoplasmic elements across a colony. Indeed, the underlying mechanistic details of how syncytia regulate cellular and molecular processes spatiotemporally across a colony are largely unexplored. Here, we implemented a strategy to analyze the relative fitness of different nuclear populations in syncytia of Neurospora crassa , including nuclei with loss-of-function mutations in essential genes, based on production of multinucleate asexual spores using flow cytometry of pairings between strains with differentially fluorescently tagged nuclear histones. The distribution of homokaryotic and heterokaryotic asexual spores in pairings was assessed between different auxotrophic and morphological mutants, as well as with strains that were defective in somatic cell fusion or were heterokaryon incompatible. Mutant nuclei were compartmentalized into both homokaryotic and heterokaryotic asexual spores, a type of bet hedging for maintenance and evolution of mutational events, despite disadvantages to the syncytium. However, in pairings between strains that were blocked in somatic cell fusion or were heterokaryon incompatible, we observed a “winner-takes-all” phenotype, where asexual spores originating from paired strains were predominantly one genotype. These data indicate that syncytial fungal cells are permissive and tolerate a wide array of nuclear functionality, but that cells/colonies that are unable to cooperate via syncytia formation actively compete for resources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones

Abstract C4 plants, such as maize, strictly compartmentalize Rubisco to bundle sheath chloroplasts. The molecular basis for the restriction of Rubisco from the more abundant mesophyll chloroplasts is not fully understood. Mesophyll chloroplasts transcribe the Rubisco large subunit gene and, when normally quiescent transcription of the nuclear Rubisco small subunit gene family is overcome by ectopic expression, mesophyll chloroplasts still do not accumulate measurable Rubisco. Here we show that a combination of five ubiquitin promoter-driven nuclear transgenes expressed in maize leads to mesophyll accumulation of assembled Rubisco. These encode the Rubisco large and small subunits, Rubisco assembly factors 1 and 2, and the assembly factor Bundle sheath defective 2. In these plants, Rubisco large subunit accumulates in mesophyll cells, and appears to be assembled into a holoenzyme capable of binding the substrate analog CABP (carboxyarabinitol bisphosphate). Isotope discrimination assays suggest, however, that mesophyll Rubisco is not participating in carbon assimilation in these plants, most probably due to a lack of the substrate ribulose 1,5-bisphosphate and/or Rubisco activase. Overall, this work defines a minimal set of Rubisco assembly factors in planta and may help lead to methods of regulating the C4 pathway.

Plant Sciences↗
DOE OSTI2024

Investigating biological nitrogen fixation via single-cell transcriptomics

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

Lotus japonicus↗
DOE OSTI2022

Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution

Background. The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus. Methods. We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals. Results. The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. Conclusions. Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism

The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae 's cellular affinity for CO 2 is stronger than the affinity of its rubisco for CO 2 . This finding provided additional evidence that C. merolae operates a CCM while lacking the structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM, distinct from those we have seen previously described in detail. The results of our modeling supported the feasibility of this proposed minimal and non-canonical CCM in C. merolae . To facilitate the robust modeling of this process, we measured and incorporated physiological and enzymatic parameters into the model. Additionally, we trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met the experimentally derived criteria for functional carbon concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO 2 membrane permeability. Our exploration thus suggested that a non-canonical CCM could exist in C. merolae and illuminated the essential features generally necessary for CCMs to function.

Steensma, Anne K. [Michigan State Univ., East Lans↗
DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗
DOE OSTI2021

Radon Kinetics in a Basement Space Measured with Different Devices

Although indoor monitoring of radon and benchmarking of radon measurement devices remain important research topics, few intercomparisons of active radon measurement devices have been performed under realistic conditions, let alone dynamic ones enabling comparison of their transient behavior. Five different radon monitors were therefore placed in a poorly ventilated basement space under three different conditions: 24 h under a steady, elevated radon level, 24 h with fans turned on to produce a radon washout transient, and 9 d with fans turned off for a radon buildup transient. Resulting radon concentrations varied between ~200 and ~2,000 Bq m -3 . Accuracy of the devices were evaluated using root-mean-square error, and ventilation data were fit to first order linear compartmental models. To more accurately model behaviors such as cyclic diurnal variations, the source term corresponding to entry of radon from soil into the basement was considered to be non-constant, as it is likely to vary drastically with both the indoor-outdoor pressure differential and soil concentration variations. Here, the improved radon washout model fit very well with the measurements. Despite a wide variety in list prices, all devices performed similarly during transients and at different radon concentrations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Quantifying the basic reproduction number and underestimated fraction of Mpox cases worldwide at the onset of the outbreak

In 2022, there was a global resurgence of mpox, with different clinical-epidemiological features compared with previous outbreaks. Sexual contact was hypothesized as the primary transmission route, and the community of men having sex with men (MSM) was disproportionately affected. Because of the stigma associated with sexually transmitted infections, the real burden of mpox could be masked. We quantified the basic reproduction number (R 0 ) and the underestimated fraction of mpox cases in 16 countries, from the onset of the outbreak until early September 2022, using Bayesian inference and a compartmentalized, risk-structured (high-/low-risk populations) and two-route (sexual/non-sexual transmission) mathematical model. Machine learning (ML) was harnessed to identify underestimation determinants. Estimated R 0 ranged between 1.37 (Canada) and 3.68 (Germany). The underestimation rates for the high- and low-risk populations varied between 25–93% and 65–85%, respectively. The estimated total number of mpox cases, relative to the reported cases, is highest in Colombia (3.60) and lowest in Canada (1.08). In the ML analysis, two clusters of countries could be identified, differing in terms of attitudes towards the 2SLGBTQIAP+ community and the importance of religion. Given the substantial mpox underestimation, surveillance should be enhanced, and country-specific campaigns against the stigmatization of MSM should be organized, leveraging community-based interventions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Walking the ‘design–build–test–learn’ cycle: flux analysis and genetic engineering reveal the pliability of plant central metabolism

Oilseeds are of great economic importance for food and animal feed and their contribution to renewable energy production. Soybean seeds (Glycine max (L.) Merr.) contain c. 40% protein, 20% oil, and 30% carbohydrate (Song et al., 2023). Due to the massive scale of soybean production worldwide, even small improvements in seed protein and oil content make economic sense (Song et al., 2023). Successful manipulation of seed composition largely depends on a thorough understanding of the processes and pathways involved in the biosynthesis of fatty acids and amino acids, which are the building blocks of lipids and proteins. Rational engineering of the synthesis of storage reserves, that is, the rerouting of metabolic flux in central metabolism, is difficult to accomplish due to the complexity of the central metabolic network, the intricate regulation of its enzymes at multiple levels, and the often-unpredictable effects of genetic manipulation (Sweetlove et al., 2017). Therefore, the advancement of our understanding of central metabolism and its control of carbon partitioning requires following an iterative ‘design–build–test–learn’ (DBTL) cycle (Lin & Eudes, 2020) where metabolic flux analysis and hypothesis testing by transgenic approaches are important components. Previous metabolic studies on soybeans using isotopic tracers and metabolic flux analysis have provided insight into how lipid and protein biosynthesis occurs simultaneously during seed development (Allen et al., 2009; Allen & Young, 2013; Kambhampati et al., 2021). In an article published in this issue of New Phytologist, Morley et al. (2023; 1834–1851) put the insights they have gained into the delivery of metabolic precursors and energy cofactors to oil synthesis to the test and arrive at a successful metabolic engineering design. They show that an increase in seed oil content in soybeans can be achieved by overexpression of malic enzyme (ME) during seed development. Malic enzyme refers to a class of decarboxylating malate dehydrogenase enzymes that oxidize malate with NAD + or NADP + as redox cofactor while generating pyruvate and CO 2 . Like higher plants in general, soybean has distinct NADH- or NADPH-producing ME isoforms localized to the cytosol, plastid, or mitochondria (Gerrard Wheeler et al., 2016). As Morley et al. show, an increase in seed oil can be achieved in particular when a NADP+-dependent enzyme isoform (EC 1.1.1.40) is overexpressed in the plastid. Given the complex compartmentalization of pyruvate, malate, and redox metabolism (Fig. 1), increased oil production appears to depend on additional pyruvate and reducing equivalents being produced in the same compartment where de novo fatty acid biosynthesis occurs: the plastid.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Understanding the dynamic nature of plant lipid anabolic and catabolic metabolism is key to sustainable oilseed engineering

Plant-derived oils are essential sources of reduced carbon and various fatty acid (FA) structures for food, biofuels, and the oleochemical industry. Despite extensive efforts, engineering mainstream oilseed crops to produce high levels of industrially valuable unusual FAs (UFAs) remains challenging. This review synthesizes recent advances in the understanding of lipid metabolic networks, emphasizing how species-specific regulation of FA synthesis, activation, and delivery influences triacylglycerol (TAG) assembly to govern the efficiency of UFA accumulation. Key insights reveal that acyl flux through anabolic and catabolic branches of lipid metabolism is tightly controlled by enzyme substrate selectivities, diacylglycerol (DAG) pool compartmentalization, and metabolic context, including lipid remodeling and degradation pathways. Engineering success is often constrained by incompatibilities between UFA biosynthetic enzymes and endogenous host metabolism, leading to flux imbalances, futile cycles, and undesired phenotypes. We highlight emerging strategies to overcome these barriers, such as the use of UFA-selective acyltransferases, coordinated manipulation of DAG source pools, suppression of competing endogenous enzymes, and exploitation of TAG remodeling mechanisms. This integrated synthesis provides a conceptual framework for logic-based engineering of oilseeds with enhanced UFA content by offering new avenues for sustainable biomanufacturing of valuable lipids.

acyltransferase specificity↗