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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural basis for human ZBTB7A action at the fetal globin promoter

Elevated levels of fetal globin protect against β-hemoglobinopathies, such as sickle cell disease and β-thalassemia. Two zinc-finger (ZF) repressors, BCL11A and ZBTB7A/LRF, bind directly to the fetal globin promoter elements positioned at -115 and -200, respectively. Here, we describe X-ray structures of the ZBTB7A DNA-binding domain, consisting of four adjacent ZFs, in complex with the -200 sequence element, which contains two copies of four consecutive C:G base pairs. ZF1 and ZF2 recognize the 5' C:G quadruple, and ZF4 contacts the 3' C:G quadruple. Natural non-coding DNA mutations associated with hereditary persistence of fetal hemoglobin (HPFH) impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in the base pairs recognized by ZF1 and ZF2. Our results firmly establish ZBTB7A/LRF as a key molecular regulator of fetal globin expression and inform genome-editing strategies that inhibit repressor binding and boost fetal globin expression to treat hemoglobinopathies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

In many biological systems, the curvature of the surfaces cells live on influences their collective properties. Curvature should likewise influence the behavior of active colloidal particles. We show using molecular simulation of self-propelled active particles on surfaces of Gaussian curvature (both positive and negative) how curvature sign and magnitude can alter the system's collective behavior. Curvature acts as a geometrical lens and shifts the critical density of motility-induced phase separation (MIPS) to lower values for positive curvature and higher values for negative curvature, which we explain theoretically by the nature of parallel lines in spherical and hyperbolic space. Curvature also fluidizes dense MIPS clusters due to the emergence of defect patterns disrupting the crystalline order inside the clusters. Using our findings, we engineer three confining surfaces that strategically combine regions of different curvature to produce a host of novel dynamical behaviors, including cyclic MIPS on spherocylinders, directionally biased cyclic MIPS on spherocones, and position dependent cluster fluctuations on metaballs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Construction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloides

A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides. Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm 3 ) capable of generating an electron density of greater than 10 13 cm –3 was constructed to produce reactive species (N 2 *, N 2 +, O, OH, and H α ) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. In conclusion, this compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dissecting components of the Campylobacter jejuni fetMP-fetABCDEF gene cluster under iron limitation

Campylobacter jejuni is a leading cause of bacterial gastroenteritis worldwide. Acute infection can be an antecedent to highly debilitating long-term sequelae. The expression of iron acquisition systems is vital for C. jejuni to survive the low iron availability within the human gut. The C. jejuni fetMP-fetABCDEF gene cluster is known to be upregulated during human infection and under iron limitation. While FetM and FetP have been functionally linked to iron transport in prior work, here we assess the contribution of each of the downstream genes (fetABCDEF) to C. jejuni growth during both iron-depleted and iron-replete conditions. Significant growth impairment was observed upon disruption of fetA, fetB, fetC, and fetD, suggesting a role in FetMP-mediated iron acquisition for each encoded protein. FetA expression was not dependent on the presence of FetB, FetC, FetD, FetE, or FetF. The functions of the putative thioredoxins FetE and FetF were redundant under iron-limited growth, requiring a double deletion (ΔfetEF) to exhibit a growth defect. C. jejuni FetE was expressed, and the structure was solved to 1.50 Å, revealing structural similarity to thiol-disulfide oxidases. Functional characterization in biochemical assays showed that FetE reduced insulin at a slower rate than Escherichia coli Trx and that together, FetEF promoted substrate oxidation in cell extracts, suggesting that FetE (and presumably FetF) are oxidoreductases that can mediate oxidation in vivo. This study advances our understanding of the contributions of the fetMP-fetABCDEF gene cluster to virulence at a genetic and functional level, providing foundational knowledge toward mitigating C. jejuni-related morbidity and mortality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation

Cancer immunotherapies often modulate macrophage effector function by introducing either targeting antibodies that activate Fcγ receptors (FcγRs) or blocking antibodies that disrupt inhibitory SIRPα-CD47 engagement. However, how these competing signals are integrated is poorly understood, raising questions about how to effectively titrate immune responses. Here, we find that macrophage phagocytic decisions are regulated by the ratio of activating ligand to inhibitory ligand over a broad range of absolute molecular densities. Using both endogenous and chimeric receptors, we show that activating:inhibitory ligand ratios of at least 10:1 are required to promote phagocytosis of model antibody-opsonized CD47-inhibited targets and that lowering that ratio reduces FcγR phosphorylation because of inhibitory phosphatases recruited to CD47-bound SIRPα. We demonstrate that ratiometric signaling is critical for phagocytosis of tumor cells and can be modified by blocking SIRPα, indicating that balancing targeting and blocking antibodies may be important for controlling macrophage phagocytosis in cancer immunotherapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication

All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Surface Treatment Strategies for Mitigating Gas Hydrate & Asphaltene Formation, Growth, and Deposition in Flowloops

Abstract Numerous solids including gas hydrates, waxes, and asphaltenes have the potential to form in the production lines of gas and oil fields. This creates a highly non-ideal scenario as the accumulation of said species leads to flow assurance issues, especially with long-term processes like deposition. Since an ever-increasing amount of material is deposited in place at the pipe surface, production stoppage or active mitigation efforts become inevitable. The latter production issues result in increased safety risks and operational expenditures. Therefore, a cost-effective, passive deposition mitigation technology, such as a pipeline coating or surface treatment is especially appealing. The ability to address multiple pipeline flow assurance issues simultaneously without actively disrupting production would represent a dramatic step forward in this area. This study is part of a long-term ongoing effort that evaluates the performance and application of an omniphobic surface treatment for solids deposition prevention in industrially relevant systems. In particular, this specific work concentrates on the efficacy and robustness of the treatment under fully flowing conditions. The apparatuses utilized for this include two flowloops: a lab-scale, high-pressure flowloop for gas hydrate and surface treatment durability studies, and a bench-scale, atmospheric pressure loop for crude oil and asphaltene experiments. Film growth in high-pressure flowloop tests corroborated previous reports of delayed gas hydrate nucleation observed in rocking cells. Without the aid of the memory effect, treated oil-dominated experiments never experienced hydrate formation, spending upwards of a week in the hydrate stability zone (at the subcooled/fluid test conditions). Subsequent tests which utilized the memory effect then revealed that the hydrate formation rate reduced in the presence of the surface treatment compared to a bare stainless-steel surface. This testing was part of a larger set of trials conducted in the flowloop, which lasted about one year. The surface treatment durability under flowing conditions was evaluated during this time. Even after experiencing ∼4000 operating hours and 2 full pressure cycles, no evidence of delamination or damage was detected. Finally, as part of an extension to previous work, corroded surface asphaltene deposition experiments were performed in a bench-top flowloop. Treated experiments displayed an order of magnitude reduction in both total oil (all fractions of crude oil) and asphaltene fraction deposited.

03 NATURAL GAS↗
DOE OSTI2024

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

How KRAS Mutations Impair Intrinsic GTP Hydrolysis: Experimental and Computational Investigations

Oncogenic KRAS mutations impair GTP hydrolysis and increase the active GTP-bound KRAS population, which leads to growth-factor-independent cell proliferation and survival of cancer cells. Despite notable successes of small-molecule inhibitors in the treatment of KRASG12C cancer, many of these small-molecule inhibitors preferentially bind to inactive (GDP-bound) mutant KRAS, whose availability is limited by the slow rate of intrinsic GTP hydrolysis. A better understanding of how KRAS mutations impair intrinsic hydrolysis is important for designing more effective small-molecule therapeutics. In this work, experimental and computational approaches were utilized to investigate how the most important oncogenic mutations affect the intrinsic hydrolysis of GTP. Here, we found that Q61H, G12V, and G12R mutations impair intrinsic hydrolysis by around 7-fold, 9-fold, and more than 20-fold, respectively, whereas G12A, G12C, G12D, and G13D have less effect. Based on mechanistic investigations, we propose that KRAS mutations impair intrinsic hydrolysis by disrupting the interactions needed to align the nucleophilic water molecule with GTP for nucleophilic attack. These results can assist small-molecule inhibitor design and also benefit the development of other therapeutic strategies, such as rescuing hydrolysis.

Ab Initio↗
DOE OSTI2022

Circadian rhythmicity of amyloid‐beta‐related molecules is disrupted in the choroid plexus of a female Alzheimer's disease mouse model

Abstract The choroid plexus (CP) is part of the blood‐cerebrospinal fluid barrier (BCSFB) and was recently described as an important component of the circadian clock system. It is the principal source of cerebrospinal fluid (CSF) and responsible for the synthesis and secretion of various neuroprotective peptides including those involved in amyloid‐β (Aβ) transport/degradation, contributing to Aβ homeostasis. Inadequate Aβ metabolic clearance and transport across the BCSFB have been associated with circadian dysfunctions in Alzheimer's disease (AD) patients. To investigate whether AD pathology influences Aβ scavengers circadian expression, we collected CP at different time points from an AD mouse model (APP/PS1) (female and male animals, aged 6‐ and 12‐months‐old) and analyzed their mRNA expression by Real‐time RT‐PCR. Only angiotensin‐converting enzyme (Ace) expression in 6‐month‐old female wild‐type mice and transthyretin (Ttr) expression in 12‐month‐old female wild‐type mice presented significant rhythmicity. The circadian rhythmicity of Ace and Ttr, prompt us to analyze the involvement of circadian rhythm in Aβ uptake. A human CP papilloma (HIBCPP) cell line was incubated with Aβ‐488 and uptake was evaluated at different time points using flow cytometry. Aβ uptake displayed circadian rhythmicity. Our results suggest that AD might affect Aβ scavengers rhythmicity and that Aβ clearance is a rhythmic process possibly regulated by the rhythmic expression of Aβ scavengers.

Furtado, André↗
DOE OSTI2021

Hydrophobe Containing Polypeptoids Complex with Lipids and Induce Fusogenesis of Lipid Vesicles

The hydrophobic effect of alkyl group insertion into phospholipid bilayers is exploited in modifying and modulating vesicle structure. We show that amphiphilic polypeptoids (peptide mimics) with n-decyl side chains, which we term as hydrophobe-containing polypeptoids (HCPs), can insert the alkyl hydrophobes into the membrane bilayer of phospholipid-based vesicles. Such insertion leads to disruption of the liposomes and the formation of HCP–lipid complexes that are colloidally stable in aqueous solution. Interestingly, when these complexes are added to fresh liposomes, remnant uncomplexed hydrophobes (the n-decyl groups) bridge liposomes and fuse them. The fusion leads to the engulfing of liposomes and the formation of multilayered vesicles. The morphology of the liposome system can be changed from stopping fusion and forming clustered vesicles to the continued formation of multilayered liposomes simply by controlling the amount of the HCP–lipid complex added. The entire procedure occurs in aqueous systems without the addition of any other solvents. There are several implications to these observations including the biological relevance of mimicking fusogenic proteins such as the SNARE proteins and the development of new drug delivery technologies to impact delivery to cell organelles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

New Views of Old Proteins: Clarifying the Enigmatic Proteome

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we offer potential futures for a next generation of disruptive approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity

Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Self-Propulsion Enhances Polymerization

Self-assembly is a spontaneous process through which macroscopic structures are formed from basic microscopic constituents (e.g., molecules or colloids). By contrast, the formation of large biological molecules inside the cell (such as proteins or nucleic acids) is a process more akin to self-organization than to self-assembly, as it requires a constant supply of external energy. Recent studies have tried to merge self-assembly with self-organization by analyzing the assembly of self-propelled (or active) colloid-like particles whose motion is driven by a permanent source of energy. Here we present evidence that points to the fact that self-propulsion considerably enhances the assembly of polymers: self-propelled molecules are found to assemble faster into polymer-like structures than non self-propelled ones. The average polymer length increases towards a maximum as the self-propulsion force increases. Beyond this maximum, the average polymer length decreases due to the competition between bonding energy and disruptive forces that result from collisions. The assembly of active molecules might have promoted the formation of large pre-biotic polymers that could be the precursors of the informational polymers we observe nowadays.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Non-linear MHD modelling of transients in tokamaks: a review of recent advances with the JOREK code

Transient magneto-hydrodynamic (MHD) events like edge localized modes (ELMs) or disruptions are a concern for magnetic confinement fusion power plants. Research with the MHD code JOREK towards understanding control of such instabilities is reviewed here in a concise way to provide a complete overview, while we refer to the original publications for details. Experimental validation for unmitigated vertical displacement events progressed. The mechanism of vertical force mitigation by impurity injection was identified. Two-way eddy current coupling to CARIDDI was completed. Shattered pellet injection was simulated in JET, KSTAR, ASDEX Upgrade (AUG) and ITER. Benign runaway electron beam termination in JET and ITER was studied. Coupling of kinetic REs to the MHD is ongoing and a virtual RE synchrotron radiation diagnostic was developed. Regarding pedestal physics, regimes devoid of large ELMs in AUG were simulated and predictive JT60-SA simulations are ongoing. For ELM suppression by resonant magnetic perturbations (RMPs), AUG, ITER and EAST simulations were performed. A free boundary RMP model was validated against experiments. Evidence for penetrated magnetic islands at the pedestal top based on AUG experiments and simulations was found. Simulations of the naturally ELM-free quiescent H-mode in AUG and HL-3 show external kink mode formation prevents pedestal build-up towards an ELM within windows of the edge safety factor. With kinetic neutral particles, high field side high density formation in ITER was simulated and with kinetic impurities, tungsten transport in AUG RMP plasmas was studied. To capture turbulent transport, electro-static full-f particle in cell models for ion temperature gradient and trapped electron modes were established and benchmarked. Application to RMP plasmas shows enhanced turbulence in comparison to unperturbed states. Energetic particle interactions with MHD were studied. Flux pumping that prevents the safety factor on axis from dropping below unity was simulated. First non-linear stellarator applications include current relaxation in $l$ = 2 stellarators, while verification for advanced stellarators progresses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Impact of Dilute DIO Additive on Local Microstructure of Fluorinated, pNDI‐Based Polymer Solar Cells

The performance of all‐polymer solar cells is often enhanced by incorporating solvent additives during solution processing. Here, in particular, blends based on the model all‐polymer system PBDBT:N2200 have been shown to have increased short‐circuit current and fill factor when processed with dilute diiodooctane (DIO). However, the morphological mechanism that drives the increase in performance is often not well understood due to limitations in common characterization techniques. In this study, it is shown that a combination of X‐ray techniques with cryogenic high‐resolution transmission electron microscopy (HRTEM) analysis can provide a quantitative and spatially resolved picture of polymer chain orientation and alignment in all‐polymer blends. It is found that DIO induces vertical phase separation in PBDBT‐2F:F‐N2200 and increases donor crystallite thickness in the pi‐stacking direction leading to an acceptor‐rich film surface. However, it is also shown that DIO does not disrupt the formation of face‐on donor–acceptor interfaces. These findings suggest that dilute DIO primarily affects crystalline domain formation in single component regions as opposed to mixed regions; thus, dilute DIO can impact vertical charge transport pathways without sacrificing donor–acceptor interfacial connectivity.

Cheng, Christina↗
DOE OSTI2023

Molecular insights into the evolution of woody plant decay in the gut of termites

Plant cell walls represent the most abundant pool of organic carbon in terrestrial ecosystems but are highly recalcitrant to utilization by microbes and herbivores owing to the physical and chemical barrier provided by lignin biopolymers. Termites are a paradigmatic example of an organism’s having evolved the ability to substantially degrade lignified woody plants, yet atomic-scale characterization of lignin depolymerization by termites remains elusive. We report that the phylogenetically derived termite Nasutitermes sp. efficiently degrades lignin via substantial depletion of major interunit linkages and methoxyls by combining isotope-labeled feeding experiments and solution-state and solid-state nuclear magnetic resonance spectroscopy. Exploring the evolutionary origin of lignin depolymerization in termites, we reveal that the early-diverging woodroach Cryptocercus darwini has limited capability in degrading lignocellulose, leaving most polysaccharides intact. Conversely, the phylogenetically basal lineages of “lower” termites are able to disrupt the lignin-polysaccharide inter- and intramolecular bonding while leaving lignin largely intact. These findings advance knowledge on the elusive but efficient delignification in natural systems with implications for next-generation ligninolytic agents.

59 BASIC BIOLOGICAL SCIENCES↗