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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome

Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR–Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.

Ghiotto, G↗
DOE OSTI2021

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response

The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola ( Xvh ) causes sorghum bacterial leaf streak. Despite being widespread, this disease has not been described in detail at the molecular level. We divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. Bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. To simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual RNA-seq on Xvh -infected sorghum. Consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. Surprisingly, bacterial virulence genes related to the type III secretion system (T3SS) and type III effectors (T3Es) were also most highly expressed in the resistance interaction. This expression pattern was observed at multiple time points within the sorghum- Xvh pathosystem. Further, a similar expression pattern was observed in Arabidopsis infected with Pseudomonas syringae for effector-triggered immunity via AvrRps4 but not AvrRpt2. Specific metabolites were able to repress the Xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. Taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Agentic AI and the Cyber Arms Race

Here, in this article, we examine the implications for cyberwarfare and global politics as agentic artificial intelligence becomes more powerful and enables the broad proliferation of capabilities only available to the most well-resourced actors today.

Cybersecurity↗
DOE OSTI2025

Local adaptation of both plant and pathogen: an arms‐race compromise in switchgrass rust

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host–parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a ‘host reciprocal transplant’ framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

19-LW-045 Full Length Final Report. Molecular Mechanisms of Bacterial Pathogenesis: Waging the Arms Race with Superbugs

As the current global pandemic makes abundantly clear, we need a better understanding of infectious disease to safeguard human health, the economy and global security. Modern omics techniques hold the promise of providing a comprehensive understanding of the molecular mechanisms of life, including causes of pathogenesis from infectious disease at the molecular level, but we there is a serious gap in annotation of gene function. For as much as half of the genes and gene products encoded in genomes the molecular and/or cellular function is unknown or only partially understood. Recent innovations in fluorescence microscopy for live cell imaging and genetic engineering make it possible to determine the temporal correlation between molecular events, such as a gene being expressed due to host-pathogen interaction, and cellular events, such as bacterial invasion of immune cells. This is turn allows us to gain new insight as to the molecular and cellular role of individual genes and will enable the discovery and validation of new molecular mechanisms essential for infectious disease. Knowing the molecular mechanisms of disease processes will provide new therapeutic targets or novel countermeasure strategies. We aimed to develop a lattice light sheet fluorescence microscope as a unique resource at LLNL for long time course live cell imaging experiments; to develop the reagents and cell lines needed to monitor molecular events during the course pathogenic bacteria infecting mammalian immune cells; and to demonstrate that we could capture molecular events during an infection. We fully commissioned the LLNL lattice light sheet microscope and conducted initial proof of principle imaging experiments on mammalian immune cells and pathogenic bacteria. It is clear from the experience gained that long time course live cell imaging has tremendous potential to help elucidate molecular mechanisms of host-pathogen interactions and to help annotate gene function, which would establish a basis for new countermeasures. It is also clear that if live cell imaging is to realize its full potential new data processing and analysis tools will need to be developed to facilitate analysis of molecular events within cells; new sample chambers and stages could facilitate studies with a wider range of cell and tissue types; and alternative molecular tagging methods need to be explored to enable more facile engineering of cells labeled with molecular specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes

Phage–bacteria interactions shape ecology and biogeochemistry across biomes. Resistance, arising from their evolutionary arms race, is well documented for receptor mutations, but other resistance mechanisms and their ecological implications remain unexplored. Here we isolated, sequenced and characterized 13 phage-resistant mutants of marine Cellulophaga baltica (Flavobacteriia). Mechanistically, mutations in surface proteins provided broad and complete extracellular resistance against multiple phages through decreased adsorption. Intracellular mutations affecting serine, glycine and threonine metabolism produced narrower resistance against a single phage, permitting viral DNA replication, and, in one mutant, were shown to be lipid mediated. Putative ecosystem impacts inferred from in vitro experiments include: (1) altered carbon utilization for all mutants, but especially by surface ones, (2) increased metabolite secretion for one modelled intracellular mutant (including experimentally verified acetate) and (3) increased ‘stickiness’ for all mutants, with surface mutants also sedimenting faster. Our findings highlight new resistance mechanisms and suggest that the phage–host arms race could result in ecosystem-level biogeochemical impacts in marine microorganisms.

Urvoy, Marion [Ohio State University]↗
DOE OSTI2026

Longitudinal Multi-omics Reveal Phase-Dependent Viral Adaptive Strategies and Functional Potential During Formation of Algal-bacterial Granular Sludge

Virus-host interactions within microbial aggregates critically influence microbiome function and stability, yet how physicochemical stresses shape the interactive dynamics remains largely unexplored. Here, we investigated virus–host dynamics during the transition of algal-bacterial granular sludge (ABGS) from activated sludge under continuous hydraulic shear using integrated metagenomics and metatranscriptomics. Hydraulic stress initially reduced host a-diversity, which coincided with a marked increase in viral lysogenicity. During this host diversity bottleneck, viral microdiversity increased, and genes related to virion structure and DNA packaging were under positive selection (pN/pS >1). As host diversity recovered, viral microdiversity declined, while viral anti-defense systems (ADS) significantly increased in abundance. Lagged correlation analysis revealed a significant positive correlation between viral ADS and host defense systems (DS), suggesting an evolutionary arms race. Furthermore, active lysogenic infections were accompanied by enrichment of DS and auxiliary viral genes (AVGs) involved in genetic information processing and amino acid metabolism, potentially enhancing host fitness. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and hosts during ABGS formation, providing insights into the development and maintenance of microbial structural and functional resilience in engineered ecosystems.

Qi, Huiyuan↗
DOE OSTI2021

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence

Abstract cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection 1–3 . In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP–AMP (cGAMP) 4,5 , which leads to the expression of antimicrobial genes 6,7 . In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered 8–11 . These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3 , which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively 8,12 . Although these proteins are required to prevent infection of some bacteriophages 8 , the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.

Science & Technology - Other Topics↗
DOE OSTI2024

An essential and highly selective protein import pathway encoded by nucleus-forming phage

Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here, we identify two components of this protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together, our results allow us to propose a multistep model for the Protein Import Chimallivirus pathway, where proteins are targeted to PicA by amino acids on their surface and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A template of information needs for decision-making about delaying remediation on contaminated lands to protect human health

The contamination legacy of industrialization, militarization, and nuclear arms race poses current or future risks to populations and the environment. Responsible parties and regulators make decisions regarding which sites to clean up, how, how much, and when. This study aimed to provide an information needs template to evaluate and reduce risks to human health when considering whether to initiate or delay remediation. This investigation focused on four aspects of timing and prioritization: 1) management, planning and implementation, 2) source terms, pathways, and exposures, 3) risks and receptors, and 4) external drivers. Within each type, issues were identified and described. Management class included personnel, health and safety data, funding, equipment, and structural integrity. Source term included contaminant sources, pathways, initiating events, and barriers to exposure. Risk included types and exposures to workers and general public. External drivers included regulatory framework, stakeholders, Congressional mandates, and economic and social contexts. Risk may increase over time as contamination spreads, enters aquifers, and reaches receptors, and may decline as radionuclides decay, and plumes dissipate. The overall objective was to provide a template of information that is useful to managers and regulators, and might be used by the public to understand the risks and benefits of re-prioritization cleanup.

Environmental Sciences & Ecology↗
DOE OSTI2022

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germ line-encoded monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and determined its structure in complex with the spike glycoprotein by electron cryomicroscopy (cryo-EM). We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its heavy complementarity-determining region 3 (HCDR3) loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that, because of the conserved nature of the epitope, the mAb maintains binding to viral variants B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron). Our study describes a novel conserved epitope on the NTD that is readily targeted by vaccine-induced antibody responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Opiate Sensitivity in Fruit Flies

Substance use disorder is a debilitating clinical condition in which behavioral dependence results from biological, environmental, genetic, and psychosocial factors. An epidemic surrounding the use and abuse of opioids is ravaging the world. While considerable efforts have explored the social drivers of addiction, a deeper understanding of biological causes and genetic vulnerabilities, preventative interventions, and effective treatments, have all proven elusive. This perspective article aims to remind readers that addictive natural compounds such as cocaine, nicotine, cathinone, or morphine, evolved as defensive metabolites to deter insect herbivory. The molecular mechanisms underlying motivational seeking and learning/reward show remarkable conservation since their early emergence in bilateral metazoans. An extended coevolutionary arms race subsequently weaponized these compounds into disruptors of learning, motivation, and incentivized attention. When plant chemical defenses attack insect physiology, humans are rendered susceptible due to strong conservation in the underlying molecular machinery. This perspective addresses the paradox that opiates were shaped to target insect neuropharmacology, even though this taxon appears to lack the recognized opioid receptor clade of mammals. We argue that the link is to be found in the allatostatin receptor, a basal ortholog of opioid receptors. Moreover, preliminary evidence indicates that morphine reduces Drosophila feeding and locomotion, concordant with a purported role as a defensive compound reducing herbivory. An implementation via allatostatin-mediated mechanisms is likely. This research argues for a broader heuristic perspective of substance abuse and a recognition of the evolutionary constraints that have likely shaped the biological drivers of opioid sensitivity and of its behavioral targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Of Clouds and Craters: The History of U.S. Nuclear Weapons Testing

“Now!” With that word, the Atomic Age – and the era of nuclear weapons testing – dawned. The advent of World War II’s first irresistible weapon, which had been secretly tested in the New Mexico desert in July 1945, would help hasten the inevitable: complete victory for the Allies. Codenamed Trinity, the test was the first of over a thousand conducted by the United States between 1945 and 1992. Nuclear weapons would change future clashes as well. The looming Cold War, with roots stretching all the way back to 1917, was history’s first conflict between two, major nations armed with nuclear weapons. It is clear the existence of those weapons played an important role in maintaining a tenuous peace between the United States and the Soviet Union; it is also clear nuclear weapons testing played a prominent role in fueling both the arms race and the success of deterrence. Yet, the history of nuclear weapons testing is rarely remembered, even though nuclear tests have been performed in the very recent past. Of the estimated 2,000-plus nuclear tests ever performed, the U.S. is responsible for approximately half. This is the story of U.S. full-scale nuclear weapons testing.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2020

A Whirlwind History of Cryptography

This presentation provides an overview of cryptography starting with the Spartan Scytale used extensively during the Peloponnesian wars up through present day. Cryptography and cryptanalysis developed side by side in arms race. Algorithm development stagnated pending cracking. Once a method of crypto was cracked, development took off. Cryptography and cryptanalysis drove developments in math, linguistics, information theory, and quantum theory, and pushed development of the first computers.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1974

Connective stability of nonlinear matrix systems

Consideration of stability under structural perturbations of free dynamic systems described by the differential equation dx/dt = A(t,x)x, where the matrix A(t,x) has time-varying nonlinear elements. The concept of 'connective stability' is introduced to study the structural properties of competitive-cooperative nonlinear matrix systems. It is shown that stability reliability in such systems is high and that they remain stable despite time-varying (including 'on-off') interaction among individual agents present in the system. The results obtained can be used to study stability aspects of mathematical models arising in as diverse fields as economics, biology, arms races, and transistor circuits.

Siljak, D. D.↗