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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing

Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure-guided microbial targeting of antistaphylococcal prodrugs

Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Updated distribution maps of predominant Culex mosquitoes across the Americas

Abstract Background Estimates of the geographical distribution of Culex mosquitoes in the Americas have been limited to state and provincial levels in the United States and Canada and based on data from the 1980s. Since these estimates were made, there have been many more documented observations of mosquitoes and new methods have been developed for species distribution modeling. Moreover, mosquito distributions are affected by environmental conditions, which have changed since the 1980s. This calls for updated estimates of these distributions to understand the risk of emerging and re-emerging mosquito-borne diseases. Methods We used contemporary mosquito data, environmental drivers, and a machine learning ecological niche model to create updated estimates of the geographical range of seven predominant Culex species across North America and South America: Culex erraticus , Culex nigripalpus , Culex pipiens , Culex quinquefasciatus , Culex restuans , Culex salinarius , and Culex tarsalis . Results We found that Culex mosquito species differ in their geographical range. Each Culex species is sensitive to both natural and human-influenced environmental factors, especially climate and land cover type. Some prefer urban environments instead of rural ones, and some are limited to tropical or humid areas. Many are found throughout the Central Plains of the USA. Conclusions Our updated contemporary Culex distribution maps may be used to assess mosquito-borne disease risk. It is critical to understand the current geographical distributions of these important disease vectors and the key environmental predictors structuring their distributions not only to assess current risk, but also to understand how they will respond to climate change. Since the environmental predictors structuring the geographical distribution of mosquito species varied, we hypothesize that each species may have a different response to climate change. Graphical abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Human-Building Collaboration: Toward lighting enabled collaborative system design

The profession of lighting design is evolving as contemporary lighting systems increasingly rely on cutting-edge computational technologies, sensors, and IOT systems. This trend requires designers to incorporate ideas of automation, dynamic controls, and user-system interaction into their design logic. However, real-time lighting simulations are constrained by inherent limitations arising from the reductive assumptions inevitably introduced in simulated lighting environments. This raises the question of how can designers account for the discrepancies between simulated and real lighting environments, and how can collaboration between humans and autonomous lighting systems bridge this gap. To address this question, we propose a protocol for designing collaborative interactions between humans and systems. Furthermore, this protocol builds on the Human-Lighting System Interaction Framework and demonstrates how human and system intelligence can be combined to fine-tune lighting qualities in a given space. Our paper shows how interactive lighting systems can customize lighting based on user preferences in real-time and how global lighting configurations can be adjusted over time. Specifically, we demonstrate: a) Human-system collaboration assumptions and goals, as well as how the protocol can be integrated into digitally programmable lighting systems. b) Implementations of collaboration that reveal how system autonomy, performance, and user experience are improved over short and long-term timeframes. c) How lighting design can be enhanced beyond simulation-driven design optimization capacities. The associated affordances and limitations are discussed with respect to existing lighting simulation design frameworks.

autonomous systems↗
DOE OSTI2025

User Acceptance of Shared Autonomous Vehicles

A dissertation is proposed to explore user acceptance of shared autonomous vehicles (SAVs). SAVs are facing limited user acceptance. To systematically tackle the user acceptance barriers of SAVs, the main problem can be disintegrated into two sub-problems of user acceptance of autonomous vehicles (AVs) and ridesharing. The comfort of the ride experience in AVs is a determinant of user acceptance. Understanding the influential factors and developing methodologies to quantify human comfort in AVs are essential to facilitating future research to improve human comfort in AVs. The current pooled rideshare (PR) service closely resembles the anticipated future of SAVs. Understanding why users prefer or refuse to use PR at the current stage prepares SAVs for broader acceptance in the future. Until now, a series of peer-reviewed publications have been published to achieve the technical goals. Two simulator-based user studies were conducted to instrument the research on human comfort in AVs. Statistical analysis was performed to identify the crucial vehicular behavioral factors of human comfort in AVs. The influential factors of human comfort in AVs and methodologies to quantify and detect human comfort in AVs were investigated. Two survey-based studies were deployed to facilitate the investigation of user acceptance of rideshare services. The influential factors of users' willingness to consider PR were explored and identified, and the choice behaviors in ridesharing services were comprehensively modeled and analyzed. The proposed research answers a series of fundamental questions regarding the user acceptance of SAVs. For the branch of user acceptance of AVs, the research generated guidelines for improving passenger comfort in AVs by identifying a series of autonomous driving factors of passenger comfort. The research also provides fundamental tools to estimate human comfort levels for future research and in-AV applications. For the branch of user acceptance of PR, the research provided user acceptance-aware vehicle, service, and policy design insights that can promote the usage of PR.

Su, Haotian↗
DOE OSTI2022

Chapter 20: Advances and Application of CRISPR-Cas Systems

A new gene-editing technique called clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have revolutionized genome engineering because of its high efficiency, relatively low cost, and ease of use compared with other techniques such as zinc-finger nucleases and transcription activator-like effector nucleases. CRISPR-Cas systems have transformed biological research, quickly becoming the preferred method for engineering specific genome sequences in industrially relevant microbes, important food crops, and human cells. This powerful new tool has the potential for limitless applications ranging from the treatment of human diseases to improving food security to the generation of renewable and sustainable bioproducts and biofuels. In this chapter, we will discuss advances and applications for these CRISPR-Cas systems in biological engineering.

bacterial↗
DOE OSTI2024

UPGRADE-E: Understanding Patterns Guiding Residential Adoption and Decisions about Energy Efficiency

This work represents the largest and most comprehensive dataset to-date of responses surveyed from U.S. residents regarding home modifications and energy-related decision-making, including both objective measures describing the occupants and their homes and subjective measures describing the more unpredictable human factors behind residential decision-making. First, to develop the survey, we interviewed 121 individual decision-makers within their households regarding planned or completed projects. We used the insights of these interviews to design a survey that was distributed to 10,000 households across the U.S. The overarching topics approached in the survey include descriptive information about the respondent, their household, their home, home modifications they have made, and the human cognition-based contextual factors involved in home projects and decision-making, such as preferences, motivations, barriers, and information sources. The processed data from the survey was compiled into a dataset entitled UPGRADE-E: Understanding Patterns Guiding Residential Adoption and Decisions about Energy Efficiency and represents the basis for the analyses included in this paper. The dataset represents a rich repository of home energy technology and modification decision-making results, the largest of its kind to-date. The abundance of contextual considerations within this dataset provides a robust resource for continual analysis, with possibilities for considering cross-cuts of data from a variety of perspectives.

Fuentes, Tracy L↗
DOE OSTI2024

The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS

Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Automating ridehailing services would reduce pooling, especially among women

Here, this study investigates how autonomous vehicles (AVs) could transform pooled (shared) ridehailing services, focusing on the impacts of fare reductions, the absence of drivers/staff, and psychological attributes such as trust in other passengers and privacy concerns. We distinguish between the automation of driving tasks and the removal of human driver/staff from the vehicle, providing novel insights into the factors influencing AV ridehailing adoption. Using a national survey with stated preference (SP) choice experiments and psychometric questions, we analyze the complex interactions of ridehailing fare, pooled ridehailing service quality, and latent attitudes on ridehailing choices. Our findings suggest that the elimination of drivers/staff from fully autonomous ridehailing could lead to a shift from pooled to solo rides, particularly among female travelers who may have greater concerns about trust and safety in unstaffed AVs. This study highlights the importance of addressing trust and comfort beyond fare discounts to ensure the inclusivity and widespread adoption of pooled AV ridehailing. These insights underscore the need for ridehailing providers and policymakers to prioritize trust-building measures, user-centered AV design that offers greater privacy, and dynamic pricing strategies, to ensure inclusive and widespread adoption of pooled AV services.

Autonomous vehicle↗
DOE OSTI2022

Simultaneous dissection of grain carotenoid levels and kernel color in biparental maize populations with yellow-to-orange grain

Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the US maize nested association mapping panel that have yellow to orange grain. Quantitative trait loci were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color quantitative trait loci ranging from 2.4% to 17.5%. These quantitative trait loci were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ~27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermoelectric air conditioning undergarment for personal thermal management and HVAC energy saving

Personal thermal management systems (PTMS) are highly desirable for improving individual thermal comfort and reducing indoor HVAC energy consumption. Although there have been many attempts in developing PTMS, existing PTMS are generally bulky, heavy or immobile. Besides, previous analysis on additional personal cooling and heating power required for maintaining thermal comfort in changing environments did not consider the individual difference in metabolism and the variability of comfort skin temperature with environmental conditions. In this paper, we report on the development of a novel lightweight (<1 kg) thermoelectric air conditioning undergarment system with a preferred design of branching tubing network (branching angle of 60° and diameter ratio of 0.782) for air distribution. Through thermal manikin and human subject tests, we demonstrated that the novel system is capable of providing a maximum of 15.5 W of personal cooling and 18.1 W personal heating with a coefficient of performance (COP) greater than 0.4, which is sufficient to the expansion of the indoor set-points by at least 2.2 °C (4 °F) on both sides without compromising thermal comfort and the potential saving of about 15% HVAC energy. Furthermore, our study improved the understanding of the required additional personal cooling and heating power for changing environmental conditions, which are essential guidelines for the further development of PTMS.

42 ENGINEERING↗
DOE OSTI2022

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively ‘featureless’ surface dominated by the peptide’s backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

CORSAIR: A Framework for Human Mobility Prediction through Visit Characterization and Spatial Behavior Modeling

The rapid advancement of location acquisition technologies has led to the daily collection of vast amounts of mobile trajectory data, facilitating in-depth research on human mobility and enabling more accurate mobility prediction models. However, existing methodologies often fall short in capturing the intricate dynamics of human navigation and spatial behavior. This paper addresses this gap by exploring the multifaceted relationships between individuals and their environments, considering the diverse influences of personal preferences and experiences. Some places hold sentimental value and are visited frequently, while others serve as transient points of passage. To model these differences, we introduce CORSAIR, a novel visit characterization framework that leverages visitation patterns and dwell times to delineate an individual’s relationship with specific places. CORSAIR classifies visits into seven distinct types: casual, occasional, routine, special, anchor, important, and resettling. Also, we show that explicitly recognizing these distinct visit types and incorporating nuanced visit intents into mobility prediction models leads to a substantial improvement in prediction accuracy. This distinction allows for more precise modeling of the individual’s transitions, enhancing the personalization and relevance of location-based services. Our findings suggest that a deeper understanding of the complexities of individual-environment interactions is crucial for developing effective predictive tools in mobility research.

Amichi, Licia [ORNL] (ORCID:0000000177631394)↗
DOE OSTI2020

SMART Mobility. Mobility Decision Science Capstone Report

The U.S. Department of Energy’s Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility Consortium is a multiyear, multi-laboratory collaborative, managed by the Energy Efficient Mobility Systems Program of the Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office, dedicated to further understanding the energy implications and opportunities of advanced mobility technologies and services. The first three-year research phase of SMART Mobility occurred from 2017 through 2019, and included five research pillars: Connected and Automated Vehicles, Mobility Decision Science, Multi-Modal Freight, Urban Science, and Advanced Fueling Infrastructure. A sixth research thrust integrated aspects of all five pillars to develop a SMART Mobility Modeling Workflow to evaluate new transportation technologies and services at scale. This report summarizes the work of the Mobility Decision Science Pillar. The Mobility Decision Science Pillar sought to fill gaps in existing knowledge about the human role in the mobility system including travel decision-making and technology adoption in the context of future mobility. The objective was to study how underlying preferences, needs, and contextual factors might constrain or hasten future transportation system scenarios. For information about the other Pillars and about the SMART Mobility Modeling Workflow, please refer to the relevant pillar’s Capstone Report.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are “dual-action” inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

Science & Technology - Other Topics↗
DOE OSTI2023

X-ray Crystallographic Study of Preferred Spacing by the NF-κB p50 Homodimer on κB DNA

Though originally characterized as an inactive or transcriptionally repressive factor, the NF-κB p50 homodimer has become appreciated as a physiologically relevant driver of specific target gene expression. By virtue of its low affinity for cytoplasmic IκB protein inhibitors, p50 accumulates in the nucleus of resting cells, where it is a binding target for the transcriptional co-activator IκBζ. In this study, we employed X-ray crystallography to analyze the structure of the p50 homodimer on κB DNA from the promoters of human interleukin-6 (IL-6) and neutrophil-gelatinase-associated lipocalin (NGAL) genes, both of which respond to IκBζ. The NF-κB p50 homodimer binds 11-bp on IL-6 κB DNA, while, on NGAL κB DNA, the spacing is 12-bp. This begs the question: what DNA binding mode is preferred by NF-κB p50 homodimer? To address this, we engineered a “Test” κB-like DNA containing the core sequence 5'-GGGGAATTCCCC-3' and determined its X-ray crystal structure in complex with p50. This revealed that, when presented with multiple options, NF-κB p50 homodimer prefers to bind 11-bp, which necessarily imposes asymmetry on the complex despite the symmetry inherent in both the protein and its target DNA, and that the p50 dimerization domain can contact DNA via distinct modes.

59 BASIC BIOLOGICAL SCIENCES↗