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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS2005

Removing Pathogens Using Nano-Ceramic-Fiber Filters

A nano-aluminum-oxide fiber of only 2 nanometers in diameter was used to develop a ceramic-fiber filter. The fibers are electropositive and, when formulated into a filter material (NanoCeram(TradeMark)), would attract electro-negative particles such as bacteria and viruses. The ability to detect and then remove viruses as well as bacteria is of concern in space cabins since they may be carried onboard by space crews. Moreover, an improved filter was desired that would polish the effluent from condensed moisture and wastewater, producing potable drinking water. A laboratory- size filter was developed that was capable of removing greater than 99.9999 percent of bacteria and virus. Such a removal was achieved at flow rates hundreds of times greater than those through ultraporous membranes that remove particles by sieving. Because the pore size of the new filter was rather large as compared to ultraporous membranes, it was found to be more resistant to clogging. Additionally, a full-size cartridge is being developed that is capable of serving a full space crew. During this ongoing effort, research demonstrated that the filter media was a very efficient adsorbent for DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and endotoxins. Since the adsorption is based on the charge of the macromolecules, there is also a potential for separating proteins and other particulates on the basis of their charge differences. The separation of specific proteins is a major new thrust of biotechnology. The principal application of NanoCeram filters is based on their ability to remove viruses from water. The removal of more than 99.9999 percent of viruses was achieved by a NanoCeram polishing filter added to the effluent of an existing filtration device. NanoCeram is commercially available in laboratory-size filter discs and in the form of a syringe filter. The unique characteristic of the filter can be demonstrated by its ability to remove particulate dyes such as Metanyl yellow. Its particle size is only 2 nanometers, about the size of a DNA molecule, yet the NanoCeram syringe filter is capable of retaining the dyes as the fluid is passed through the syringe, without much back-pressure. Endotoxins, which are contaminants that are part of the residue of destroyed bacteria, can cause toxic shock and are therefore of major concern in pharmaceutical products. The NanoCeram syringe filter is capable of removing greater than 99.96 percent of the endotoxins.

Tepper, Frederick↗
DOE OSTI2021

Global overview and major challenges of host prediction methods for uncultivated phages

Bacterial communities play critical roles across all of Earth’s biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, i.e., bacteriophages or “phages”. Phages can reshape bacterial communities’ structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, i.e., shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown

RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium -mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗
DOE OSTI2024

A compendium of multi-omics data illuminating host responses to lethal human virus infections

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing

The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

The chemical structure of DNA sequence signals for RNA transcription

The proposed recognition sites for RNA transcription for E. coli NRA polymerase, bacteriophage T7 RNA polymerase, and eukaryotic RNA polymerase Pol II are evaluated in the light of the requirements for efficient recognition. It is shown that although there is good experimental evidence that specific nucleic acid sequence patterns are involved in transcriptional regulation in bacteria and bacterial viruses, among the sequences now available, only in the case of the promoters recognized by bacteriophage T7 polymerase does it seem likely that the pattern is sufficient. It is concluded that the eukaryotic pattern that is investigated is not restrictive enough to serve as a recognition site.

George, D. G.↗
NASA NTRS2023

ChIPPS: Charged Information-storage Polymer Preparation System

Technological advances are required to support principal science objectives of missions to the solar system’s icy worlds to seek biosignatures of past/extant life. Sensitivity and reliability are key concerns due to small sample sizes (µL – mL) and the extraordinary import of the results. The preparation and processing of small samples can constrain limits of detection (LoDs); therefore, the Charged Information-storage Polymer Preparation System (ChIPPS) project is advancing the technologies of autonomous sample preparation and processing to add a new class of reliably detectable biosignatures: charged polymers and particles, which can be the information storage-and-transmission means for life. Specifically, we are developing an integrated microfluidic sample-processing unit to prepare icy-world samples to support complementary solid-state nanopore-based analyses: 1) charged-polymer analysis, to characterize variations in polymer chain size, shape, and charge vs. position along the chain; 2) polymer and nanoparticle sizing-and-counting, to characterize the relative abundance of polymer chains, as well as small (virus-sized) particles, by their dimensions and charge. Although no such autonomous system presently exists, such measurements can reveal the nature and abundance of charged polymers that could be used by biological systems to store and transfer information—as DNA and RNA are used terrestrially—without limitation to terrestrial nucleic acids, given that life elsewhere may utilize different information store-and-transfer moieties. Key system components include (a) a lysis unit for mechanical sample disruption; b) an ion-exchange column for charged macromolecule/nanoparticle purification; c) dialyzer to remove excess salt; d) concentrator to enhance signal; e) supporting pumps, valves, bubble traps, connectors, filters, etc.; f) interface to nanopore detection instruments.

Space Biology↗
DOE OSTI2022

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy

Treating macaques with an anti-α4β7 antibody under the umbrella of combination antiretroviral therapy (cART) during early SIV infection can lead to viral remission, with viral loads maintained at < 50 SIV RNA copies/ml after removal of all treatment in a subset of animals. Depletion of CD8+ lymphocytes in controllers resulted in transient recrudescence of viremia, suggesting that the combination of cART and anti-α4β7 antibody treatment led to a state where ongoing immune responses kept the virus undetectable in the absence of treatment. A previous mathematical model of HIV infection and cART incorporates immune effector cell responses and exhibits the property of two different viral load set-points. While the lower set-point could correspond to the attainment of long-term viral remission, attaining the higher set-point may be the result of viral rebound. Here we expand that model to include possible mechanisms of action of an anti-α4β7 antibody operating in these treated animals. We show that the model can fit the longitudinal viral load data from both IgG control and anti-α4β7 antibody treated macaques, suggesting explanations for the viral control associated with cART and an anti-α4β7 antibody treatment. This effective perturbation to the virus-host interaction can also explain observations in other nonhuman primate experiments in which cART and immunotherapy have led to post-treatment control or resetting of the viral load set-point. Interestingly, because the viral kinetics in the various treated animals differed—some animals exhibited large fluctuations in viral load after cART cessation—the model suggests that anti-α4β7 treatment could act by different primary mechanisms in different animals and still lead to post-treatment viral control. This outcome is nonetheless in accordance with a model with two stable viral load set-points, in which therapy can perturb the system from one set-point to a lower one through different biological mechanisms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Cell to Ecosystem: Understanding Methane and Associated Nutrient Cycling by Sediment Hosted Syntrophic Consortia and Their Viral Predators

The anaerobic oxidation of methane (AOM) is a significant worldwide microbial process in anoxic lake and ocean sediments, responsible for sequestering up to 80% of this greenhouse gas. Often considered a metabolism on the edge of thermodynamic probability, the impact of ANaerobic MEthane-oxidizing ‘ANME’ archaea on carbon and nutrient cycling in sediment ecosystems is far reaching. They not only serve as a sink for methane coupled to diverse electron acceptors, but also catalyze the transformation of many important nutrients including nitrogen, phosphate, and iron. While information about the potential mechanisms supporting metabolism in AOM is now available, remarkably little has been learned about their nutritional requirements, their dependencies on bacterial partners, and consequentially their ultimate impact on nutrient transformation and bioavailability within sedimentary ecosystems, and beyond. Further, the role of viruses within sediment ecosystems represents an essential but vastly understudied aspect of the transformation of carbon and nutrients by AOM. Viruses are now widely appreciated as central players in biogeochemical cycles across diverse ecosystems. These nanoscale predators have been shown to enhance the turnover of essential nutrients, thus stimulating microbial growth and environmental viruses themselves may constitute an important reservoir of nitrogen and phosphorous. Little is known about the role of viruses in methane-impacted sedimentary ecosystems, however prior genomic and microscopy evidence suggests that AOM consortia are susceptible to phage infection. The overarching scientific goal of this multi-disciplinary research proposal is to build on these recent discoveries and expand our understanding of interactions and fundamental activities involved in cycling of carbon and nutrients by syntrophic methanotrophic archaeal-bacterial consortia and associated viruses in anoxic sedimentary environments. Our three specific objectives are to 1) Quantify energy and nutrient exchange (e.g. N, P, Fe and vitamins) within AOM consortia and between ANME-bacterial partners; 2) Identify virus-host interactions associated with AOM and assess C and N transfer through viruses in methane-impacted sediment ecosystems; 3) Model energy and nutrient exchange in AOM consortia and viral-host interactions (i.e. viral activity), and their environmental distribution patterns. Our experimental emphasis cuts across scales that are important for understanding microbial and viral interactions and activities within their habitats, as well as community wide biogeochemical transformations. These research goals will be accomplished through the application of novel molecular techniques targeting DNA, RNA, proteins, and metabolites combined with a unique multi-modal analytical imaging pipeline. We will then model the ecophysiological capabilities of diverse sediment-hosted methanotrophic consortia to develop a more comprehensive understanding of the energetic and nutritional interactions between different AOM partner couplings that occur in sediments.

03 NATURAL GAS↗
DOE OSTI2020

Ribavirin targets sugar transporter 6 to suppress acquisition and transmission of rice stripe tenuivirus by its vector Laodelphax striatellus

Abstract BACKGROUND Rice stripe tenuivirus (RSV) is one of the most destructive pathogens of rice and other cereal crops. The virus is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus ) in a circulative‐propagative manner. Thus, blocking transmission by the insect vector would provide an effective strategy to prevent epidemic outbreaks of the disease. RESULTS In this study, we explored the effect of ribavirin on acquisition and transmission of the virus by specifically inhibiting the expression of sugar transporter 6 (LsSt‐6), which was recently reported as a key vector component for RSV transmission. Ribavirin at the highest concentration tested (250 μmol L ‐1 ) significantly reduced RSV acquisition and transmission efficiency by SBPHs through inhibiting LsSt‐6 messenger RNA (mRNA) level. Survival of the model insect Spodoptera frugiperda cell line (Sf9) was 95.0 ± 2.2 and 85.6 ± 2.1% after exposure to 250 μmol L ‐1 ribavirin or 8‐azaguanine, respectively. Further study confirmed that 250 μmol L ‐1 ribavirin also significantly reduced LsSt‐6 mRNA and protein levels in Sf9 cells. However, 8‐azaguanine did not significantly inhibit viral infectivity and LsSt‐6 mRNA levels in SBPH or the Sf9 cell line. CONCLUSION This result provides evidence that ribavirin has the potential to disrupt LsSt‐6 expression but not others like viral RNAs to prevent acquiring RSV, which leads to less viral accumulation in SBPH tissues and thereby lower transmission efficiency. © 2020 Society of Chemical Industry

Hajano, Jamal‐U‐Ddin↗
DOE OSTI2022

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Antiretroviral therapy for HIV and intrahepatic hepatitis C virus replication

HIV alters host responses to hepatitis C virus (HCV). However, the impact of antiretroviral therapy (ART) on HCV is rarely understood in relevant tissues and never before within individual hepatocytes. HIV and HCV kinetics were studied before and after ART initiation among 19 HIV/HCV co-infected persons. From five persons with the largest decline in plasma HCV RNA, liver tissues collected before and during ART, when plasma HIV RNA was undetectable, were studied. Here we used single-cell laser capture microdissection and quantitative PCR to assess intrahepatic HCV. Immunohistochemistry was performed to characterize intrahepatic immune cell populations. Plasma HCV RNA declined by 0.81 (0.52–1.60) log 10 IU/ml from a median (range) 7.26 (6.05–7.29) log 10 IU/ml and correlated with proportions of HCV-infected hepatocytes (r = 0.89, P = 2 × 10 -5 ), which declined from median (range) of 37% (6–49%) to 23% (0.5–52%) after plasma HIV clearance. Median (range) HCV RNA abundance within cells was unchanged in four of five participants. Liver T-cell abundance unexpectedly decreased, whereas natural killer (NK) and NK T-cell infiltration increased, correlating with changes in proportions of HCV-infected hepatocytes (r = -0.82 and r = -0.73, respectively). Hepatocyte expression of HLA-E, an NK cell restriction marker, correlated with proportions of HCV-infected hepatocytes (r = 0.79). These are the first data to show that ART control of HIV reduces the intrahepatic burden of HCV. Furthermore, our data suggest that HIV affects the pathogenesis of HCV infection by an NK/NK T-cell-mediated mechanism that may involve HLA-E and can be rescued, at least in part, by ART.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Substituent size versus metal binding of inhibitors with variants of influenza endonuclease

The influenza virus causes a significant burden of illness each year. Although vaccination is the most effective method to prevent seasonal influenza infection, viral escape mechanisms make vaccine composition difficult to predict. Antivirals are crucial for decreasing rates of morbidity and mortality from influenza viral infection. The newest anti-influenza drugs target the RNA-dependent RNA polymerase acidic N-terminal (PA N ) endonuclease, a critical component of influenza viral replication machinery. This study examines the structure of inhibitors of PAN that utilize a hydroxypyridinone-based metal-binding pharmacophore (MBP). Specifically, this report explores how the size of substituent groups impacts the binding conformation and affinity of a series of compounds against both wild-type (WT) and resistance mutant strains, I38T and E23K. Co-crystal structures revealed that the distance between compounds and enzyme residue 38 was conserved to maintain strong interactions, resulting in deviations from ideal coordination geometries at the active site metal centers. This suggests the interactions with residue 38 with each compound is important and can impact inhibitor potency as a consequence of distortions in the metal binding geometry of the compounds.

Endonuclease↗
DOE OSTI2024

COVID-19 trends at the University of Tennessee: predictive insights from raw sewage SARS-CoV-2 detection and evaluation and PMMoV as an indicator for human waste

Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it’s not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage. This was done to investigate the correlations between SARS-CoV-2 RNA load, both with and without PMMoV normalization, and various parameters, including active COVID-19 cases, self-isolations, and their combination among all student residents. Significant positive correlations between SARS-CoV-2 RNA load a week prior, during the monitoring week, and the subsequent week with active cases. Despite these correlations, normalization by PMMoV does not enhance these associations. These findings suggest the potential utility of SARS-CoV-2 RNA load as an early warning indicator and provide valuable insights into the application and limitations of WBE for COVID-19 surveillance specifically within the context of raw sewage on university campuses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Inhibition of tick-borne encephalitis virus in cell cultures by ribavirin

Tick-borne encephalitis virus (TBEV) belonging to arboviruses is a major member of zoonotic pathogens. TBEV infection causes severe human encephalitis without specific antiviral drugs. Due to its use of antiviral drug against a wide range of viruses, we investigated antiviral effect of ribavirin against TBEV in susceptible human cell lines A549 and SH-SY5Y. Ribavirin displayed minor cytotoxicity on multiple cell lines. Ribavirin obviously impaired TBEV replication and protected the infected cells from cytopathic effect. Importantly, ribavirin markedly inhibited TBEV propagation, as evidenced by impairment of TBEV production and viral RNA replication. Treatment with ribavirin (co-treatment and post-treatment) led to a dose-dependent reduction in TBEV titers as well as the viral RNA levels. Antiviral protein myxovirus resistance A mRNA expression was significantly up-regulated and signal transducer and activator of transcription 3 was activated in TBEV-infected A549 cells upon the ribavirin treatment. Induction of inflammatory cytokine tumor necrosis factor alpha by TBEV was decreased in A549 cells with the treatment of ribavirin, whereas interleukin 1 beta release appeared to be unaffected. These results suggest that ribavirin might represent a promising safe and effective antiviral drug against TBEV.

Tang, Wan-Da↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗