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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 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

In vivo mapping of mutagenesis sensitivity of human enhancers

Distant-acting enhancers are central to human development1. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease2. Here we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers that are active in the developing brain, heart, limb and face, we created over 1,700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-base-pair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modelling, we annotated critical nucleotides at the base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes in in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features that are required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

Kosicki, Michael↗
DOE OSTI2022

Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies

Proteins including FUS, hnRNPA2, and TDP-43 reversibly aggregate into amyloid-like fibrils through interactions of their low-complexity domains (LCDs). Mutations in LCDs can promote irreversible amyloid aggregation and disease. We introduce a computational approach to identify mutations in LCDs of disease-associated proteins predicted to increase propensity for amyloid aggregation. We identify several disease-related mutations in the intermediate filament protein keratin-8 (KRT8). Atomic structures of wild-type and mutant KRT8 segments confirm the transition to a pleated strand capable of amyloid formation. Biochemical analysis reveals KRT8 forms amyloid aggregates, and the identified mutations promote aggregation. Aggregated KRT8 is found in Mallory–Denk bodies, observed in hepatocytes of livers with alcoholic steatohepatitis (ASH). We demonstrate that ethanol promotes KRT8 aggregation, and KRT8 amyloids co-crystallize with alcohol. Lastly, KRT8 aggregation can be seeded by liver extract from people with ASH, consistent with the amyloid nature of KRT8 aggregates and the classification of ASH as an amyloid-related condition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mapping of inhomogeneous quasi-3D electrostatic field in electro-optic materials

Abstract This paper describes a new method for direct measurement and evaluation of the inhomogeneous electrostatic vector field with translational symmetry in electro-optic materials exhibiting the Pockels effect. It is based on the evaluation of maximum transmittance of low intensity light passing through a sample under a voltage bias. Here, the sample is located between rotating crossed polarizers, and camera images are obtained at each point to determine the electric field. The evaluation procedure is demonstrated using data acquired on a CdZnTeSe quasi-hemispheric semiconductor gamma-ray detector. In addition to CdTe-related compounds, the method can be used for various other materials showing $$\overline{4}3m$$ 4 ¯ 3 m symmetry such as GaAs, CdTe, GaP, 3C-SiC, and ZnS. Furthermore, it can be generalized to other crystalline materials showing the Pockels effect. The method can be used to probe the space charge and the electric field in several kinds of electronic components and devices, as well as provide useful data on the role of defects, contact configurations and other surface and bulk inhomogeneities in the material that can affect the distribution of the internal electric field.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Magnetic field mapping of inaccessible regions using physics-informed neural networks

A difficult problem concerns the determination of magnetic field components within an experimentally inaccessible region when direct field measurements are not feasible. In this paper, we propose a new method of accessing magnetic field components using non-disruptive magnetic field measurements on a surface enclosing the experimental region. Magnetic field components in the experimental region are predicted by solving a set of partial differential equations (Ampere’s law and Gauss’ law for magnetism) numerically with the aid of physics-informed neural networks (PINNs). Prediction errors due to noisy magnetic field measurements and small number of magnetic field measurements are regularized by the physics information term in the loss function. We benchmark our model by comparing it with an older method. The new method we present will be of broad interest to experiments requiring precise determination of magnetic field components, such as searches for the neutron electric dipole moment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography

Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States

Abstract Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E ( mcyE ) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis . Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Abstract The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N -terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N - and O - glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Integrative path modeling and QTL mapping identify maturity, stem strength, and cell wall composition driving lettuce resistance to Sclerotinia minor

Lettuce ( Lactuca sativa ) is highly vulnerable to Sclerotinia minor , the pathogen causing lettuce drop. Breeding for resistance is the most effective control strategy; however, full resistance has not been achieved, and current partial resistance sources are often linked with undesirable traits, such as early bolting. This study aimed to unravel the genetic basis of partial resistance to S. minor and its relationship with plant maturity (bolting), stem mechanical strength (SMS), and cell wall composition (CWC) using a recombinant inbred line (RIL) population derived from a cross between the susceptible iceberg cv. ‘Salinas’ and the resistant oil-seed accession PI 251246. Field evaluations indicated that resistance was linked to earlier bolting, stronger stems, and higher pentose content. Path analysis demonstrated that earlier-maturing plants exhibited increased resistance through enhanced SMS and modified CWC, particularly with higher xylose and lower arabinose levels. Further analysis indicated a significant relationship between syringyl lignin content and resistance, especially in plants with varying bolting responses. Three key quantitative trait loci (QTLs) on linkage groups (LG) 2, 6, and 7 were consistently associated with resistance, bolting, and SMS. Importantly, residual QTL analysis revealed that the resistance locus on LG7 acted independently of maturity, suggesting a distinct resistance mechanism. Callose synthase emerged as a key candidate gene within the LG7 resistance QTL, located near - but distinct from - genes associated with plant maturity and flowering. These findings provide valuable insights into decoupling resistance from early bolting, suggesting a pathway for breeding lettuce cultivars with improved disease resistance and delayed bolting.

Lactuca↗
DOE OSTI2021

Mapping classes of carbon

With rising fossil fuel consumption and ongoing land cover change, humanity is burning through its remaining carbon budget. Here, recent work puts a ‘Do not disturb’ sign on biospheric carbon we can’t afford to lose.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Single-molecule reaction mapping uncovers diverse behaviours of electrocatalytic surface Pd–H intermediates

Many vital electrocatalytic transformations hinge on reactive surface metal–hydrogen intermediates (M–H*), yet the low concentration and transient nature of such intermediates present formidable challenges to in-depth investigation. Here we use single-molecule super-resolution reaction imaging to directly probe surface palladium–hydrogen (Pd–H*) intermediates on individual palladium nanocubes during electrocatalytic hydrogen evolution. Our approach visualizes hydrogen spillover from palladium to the surrounding substrate surface over hundreds of nanometres away and dissects substantial inter- and intraparticle heterogeneity. Through Gaussian-broadening kinetic analysis, we reveal that ensemble-averaged measurements systematically overestimate the stability of Pd–H*. Moreover, we resolve three subpopulations of palladium nanocubes with distinct reactivity features, uncovering critical correlations between intermediate stability, hydrogenation reactivity and transition-state properties. Finally, our findings highlight the necessity of single-particle resolution for capturing the intrinsic complexity of electrocatalysts; our approach is also broadly applicable to interrogate surface-reactive intermediates across a wide array of electrocatalytic pathways.

electrocatalysis↗
DOE OSTI2023

Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase

Abstract CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mapping the nonequilibrium order parameter of a quasi-two dimensional charge density wave system

The driving force of a charge density wave (CDW) transition in quasi-two dimensional systems is still debated, while being crucial in understanding electronic correlation in such materials. Here we use femtosecond time- and angle-resolved photoemission spectroscopy combined with computational methods to investigate the coherent lattice dynamics of a prototypical CDW system. The photo-induced temporal evolution of the periodic lattice distortion associated with the amplitude mode reveals the dynamics of the free energy functional governing the order parameter. Our approach establishes that optically-induced screening rather than CDW melting at the electronic level leads to a transiently modified potential which explains the anharmonic behaviour of the amplitude mode and discloses the structural origin of the symmetry-breaking phase transition.

electronic properties and materials↗
DOE OSTI2021

Global urban growth between 1870 and 2100 from integrated high resolution mapped data and urban dynamic modeling

Long term, global records of urban extent can help evaluate environmental impacts of anthropogenic activities. Remotely sensed observations can provide insights into historical urban dynamics, but only during the satellite era. Here, we develop a 1 km resolution global dataset of annual urban dynamics between 1870 and 2100 using an urban cellular automata model trained on satellite observations of urban extent between 1992 and 2013. Hindcast (1870–1990) and projected (2020–2100) urban dynamics under the five Shared Socioeconomic Pathways (SSPs) were modeled. We find that global urban growth under SSP5, the fossil-fuelled development scenario, was largest with a greater than 40-fold increase in urban extent since 1870. The high resolution dataset captures grid level urban sprawl over 200 years, which can provide insights into the urbanization life cycle of cities and help assess long-term environmental impacts of urbanization and human–environment interactions at a global scale.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Mapping the effects of physical and chemical reduction parameters on local atomic distributions within bimetallic nanoparticles

Bimetallic nanoparticles prove advantageous over their monometallic counterparts due to the tunable, hybrid properties that result from combining different atomic species in a controlled way. The favorable optical and catalytic properties resulting from AgAu nanoparticle formation have been widely attributed to the existence of Ag–Au bonds, the maximization of which assumes the formation of a homogeneous alloy. Despite the importance of atomic scale structure in these systems, synthetic studies are typically not paired with structural characterization at the atomic scale. Herein, a comprehensive synthetic exploration of physical and chemical reduction parameters of resulting nanoparticle products is complemented with thorough X-ray characterization to probe how these parameters affect atomic scale alloy distributions within AgAu nanoparticles. Presented evidence shows Ag is substantially underincorporated into nanoparticle constructs compared with solution Ag : Au ratios regardless of precursor :reductant ratio or volume of reductant added. Both Ag and Au exhibit significant local clustering, with Ag distributed preferentially towards the nanoparticle surface. Most significantly, the results of this investigation suggest that reduction parameters alone can affect the local alloy distributions and homogeneity within bimetallic nanoparticles, even when the ratio of metallic precursors remains constant. Overall, this investigation presents the ability to control alloy distributions using kinetics and provides new considerations for optimizing synthetic methods to produce functional bimetallic nanoparticles.

77 NANOSCIENCE AND NANOTECHNOLOGY↗