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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

2.7 Å cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity

In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo–electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ozone Gas: Scientific Justification and Practical Guidelines for Improvised Disinfection using Consumer-Grade Ozone Generators and Plastic Storage Boxes

Here, we describe direct measurements of ozone concentration achievable in small enclosed containers (plastic storage boxes) for use as improvised decontamination systems for small articles such as disposable PPE (N95 masks, nitrile gloves, etc.), clothing, mail and small packages, food, and other miscellaneous articles. The emphasis is on the reliable and sustained generation of ozone gas concentrations of sufficient concentration and duration to create an effective virucidal environment to achieve more than 95% to 99% viral inactivation, based upon the data already published in the peer-review literature on this topic. The suggestion that ozone be used to inactivate virus is certainly not a new idea. Our objective in this report is to make clear that the necessary levels of ozone can be improvised using simple, easy-to-use, inexpensive, and widely available supplies, and that there is every theoretical and experimental reason to believe that this approach is as highly effective in viral inactivation by ozone as are the far more expensive, complex, cumbersome, and less available equivalent ozone (and other) disinfectant systems that have themselves become unavailable during times of pandemic crisis. Using multiple types of readily available commercial ozone generators, concentration in the tested improvised enclosure is tracked over time to assess ozone charging and decay rates, and the ozone quenching effects of items placed in the box. Generator performance is compared against published ozone dosage values for virucidal and antimicrobial activity. Bubbler and box-fan-type ozone generators were found to be effective at achieving and maintaining target concentrations of 10ppm ozone or higher, whereas automotive cigarette lighter and universal serial bus type plug in “air freshener” ozone generators could not achieve the target concentrations in these experiments. Calculations and practical guidelines for assembly and effective use of an ozone box for improvised decontamination are offered. The majority of this report is directed toward the scientific justification and rationale for this approach. The end of the document summarizes the findings and offers simplified designs for the construction and use of ozone boxes as an improvised method of disinfection.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2002

Genetic Optimization of a Tensegrity Structure

Marshall Space Flight Center (MSFC) is charged with developing advanced technologies for space telescopes. The next generation of space optics will be very large and lightweight. Tensegrity structures are built of compressive members (bars), and tensile members (strings). For most materials, the tensile strength of a longitudinal member is larger than its buckling strength; therefore a large stiffness to mass ratio can be achieved by increasing the use of tensile members. Tensegrities are the epitome of lightweight structures, since they take advantage of the larger tensile strength of materials. The compressive members of tensegrity structures are disjoint allowing compact storage of the structure. The structure has the potential to eliminate the requirement for assembly by man in space; it can be deployed by adjustments in its cable tension. A tensegrity structure can be more reliably modeled since none of the individual members experience bending moments. (Members that experience deformation in more than one dimension are much harder to model.) Structures that can be more precisely modeled can be more precisely controlled. Furthermore, an astoundingly wide variety of natural systems, including carbon atoms, water molecules, proteins, viruses, cells, tissues and even human and other living creatures are tensegrity structures. Through the process of evolution, nature continually improves the design of living creatures for the environment they live in. Since tensegrities are nature's structure of choice, it is conceivable that they have other benefits we are unaware of. A. Keane and S. Brown designed a satellite boom truss system with an enhanced vibration performance. They started with a standard truss system, then used a genetic algorithm to alter the design, while optimizing the vibration performance. An improvement of over 20,000% in frequency-averaged energy levels was obtained using this approach. In this report an introduction to tensegrity structures is given, along with a description of how to generate the nodal coordinates and connectivity of a multiple stage cylindrical tensegrity structure. A description of how finite elements can be used to develop a stiffness and mass matrix so that the modes of vibration can be determined from the eigenvalue problem is shown. A brief description of a micro genetic algorithm is then presented.

Jaime R. Taylor↗
DOE OSTI2022

Large Scale MD to Predict Epitope Regions in HIV Env [Slides]

Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Efficient facemask decontamination via forced ozone convection

The COVID-19 crisis has taken a significant toll on human life and the global economy since its start in early 2020. Healthcare professionals have been particularly vulnerable because of the unprecedented shortage of Facepiece Respirators (FPRs), which act as fundamental tools to protect the medical staff treating the coronavirus patients. In addition, many FPRs are designed to be disposable single-use devices, creating an issue related to the generation of large quantities of non-biodegradable waste. In this contribution, we describe a plasma-based decontamination technique designed to circumvent the shortages of FPRs and alleviate the environmental problems posed by waste generation. The system utilizes a Dielectric Barrier Discharge (DBD) to generate ozone and feed it through the fibers of the FPRs. The flow-through configuration is different than canonical ozone-based sterilization methods, in which the equipment is placed in a sealed ozone-containing enclosure without any flow through the mask polymer fibers. We demonstrate the rapid decontamination of surgical masks using Escherichia coli ( E. coli ) and Vesicular Stomatitis Virus (VSV) as model pathogens, with the flow-through configuration providing a drastic reduction in sterilization time compared to the canonical approach. We also demonstrate that there is no deterioration in mask structure or filtration efficiency resulting from sterilization. Finally, we show that this decontamination approach can be implemented using readily available tools, such as a plastic box, a glass tube, few 3D printed components, and the high-voltage power supply from a plasma globe toy. The prototype assembled for this study is portable and affordable, with effectiveness comparable to that of larger and more expensive equipment.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Abstract Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A chromosome-scale reference genome of trifoliate orange ( Poncirus trifoliata ) provides insights into disease resistance, cold tolerance and genome evolution in Citrus

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosomescale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/ DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/ Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2011

Rapid Detection of the Varicella Zoster Virus in Saliva

Varicella zoster virus (VZV) causes chicken pox on first exposure (usually in children), and reactivates from latency causing shingles (usually in adults). Shingles can be extremely painful, causing nerve damage, organ damage, and blindness in some cases. The virus can be life-threatening in immune-compromised individuals. The virus is very difficult to culture for diagnosis, requiring a week or longer. This invention is a rapid test for VZV from a saliva sample and can be performed in a doctor s office. The kit is small, compact, and lightweight. Detec tion is sensitive, specific, and noninvasive (no needles); only a saliva sample is required. The test provides results in minutes. The entire test is performed in a closed system, with no exposure to infectious materials. The components are made mostly of inexpensive plastic injection molded parts, many of which can be purchased off the shelf and merely assembled. All biological waste is contained for fast, efficient disposal. This innovation was made possible because of discovery of a NASA scientists flight experiment showing the presence of VZV in saliva during high stress periods and disease. This finding enables clinicians to quickly screen patients for VZV and treat the ones that show positive results with antiviral medicines. This promotes a rapid recovery, easing of pain and symptoms, and reduces chances of complications from zoster. Screening of high-risk patients could be incorporated as part of a regular physical exam. These patients include the elderly, pregnant women, and immune-compromised individuals. In these patients, VZV can be a life-threatening disease. In both high- and low-risk patients, early detection and treatment with antiviral drugs can dramatically decrease or even eliminate the clinical manifestation of disease.

Pierson, Duane L.↗
DOE OSTI2023

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

COVID-19 biomarkers based on respiratory microbiome content

COVID-19 patient care management would greatly benefit from new tools that enable accurate assessment of disease severity and stage, potentially enabling a personalized medicine approach. Detection of the SARS-CoV-2 virus itself, or even quantitation of viral loads, is not sufficient for accurate assessment of disease state beyond diagnosis of infection [eg, doi:10.1093/cid/ciaa344]. Levels of usual suspect protein biomarkers associated with host response to infection [eg, C-reactive protein (CRP); cytokines like IL-6, TNF-alpha, and IL-10; complement proteins like C3a and C5a], and of individual blood cell types (eg, leukocytes, lymphocytes, and subsets thereof), show limited correlation with disease severity and stage, with high patient-to-patient and study-to-study variability [eg, doi:10.1093/cid/ciaa248]. High-dimensional panels of biomarkers should have greater predictive power and resilience to unavoidable sources of variability; however, their assembly from proteins and cell types is extremely difficult, due to technical limitations in analyte measurement, especially with regard to starting material requirements and detection sensitivity. Host response profiling through Next Generation Sequencing (NGS) of gene expression patterns (ie, RNA-Seq) is a promising approach, but at the time of this project there were only two publicly available datasets of relevance [doi:10.1093/cid/ciaa203, doi:10.1080/22221751.2020.1747363], and close inspection of them revealed that each had at least one major flaw that severely undermined its value in supporting robust analysis of host response to SARS-CoV- 2 infection. However, the first of these studies [doi:10.1093/cid/ciaa203] fortuitously collected NGS data not only from host cells, but also from bacteria present in bronchoalveolar lavage fluid (BALF) recovered from COVID-19 patients; and because the respiratory microbiome (in terms of bacterial species content) is far less complex than the human transcriptome, the NGS data collected were sufficient to provide coverage depth supporting robust analysis. Surprisingly, the authors of the study did not carry out a detailed analysis of these data and their potential for revealing important new information about COVID-19. Therefore, we carried out a meta-analysis of the dataset as a first step in evaluating the potential for profiling of respiratory microbiome dynamics as a means of accurately assessing COVID-19 disease state.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Bemnifosbuvir: An HCV NS5B Inhibitor With Multiple Modes of Action

Bemnifosbuvir (BEM) is a potent, pan-genotypic inhibitor targeting the hepatitis C virus (HCV) NS5B polymerase. Its antiviral activity was evaluated in an ascending dose phase I clinical trial involving 30 patients treated once a day for 7 days. After treatment initiation, plasma HCV RNA declined in a biphasic manner with a mean reduction of 2.3 log 10 IU/mL after 24 hours and 4.4 log10 IU/mL by day 7 for the highest dose. Alanine aminotransferase (ALT) also normalized in most patients. We employed a multiscale mathematical model fitted to the HCV RNA and ALT dynamics to quantify the antiviral activity and evaluate the modes of action of BEM. We found that models in which BEM only acted as a typical HCV RNA polymerase inhibitor and reduced the intracellular production of HCV RNA did not fit the data as well as models in which BEM had multiple modes of action, including suppressing viral assembly and secretion and enhancing intracellular HCV RNA degradation. BEM's effectiveness in inhibiting intracellular HCV RNA production increased with dose (150 mg/day: 88.2%, 300 mg/day: 98.8%, 600 mg/day: 99.5%), while inhibition of viral assembly and release was ~95% effective regardless of dose. We observed a dose-dependent enhancement in the degradation of intracellular HCV RNA, with degradation rates 1.5-fold higher in patients receiving 300 mg/day and 2.7-fold higher in those receiving 600 mg/day than in patients receiving 150 mg/day. No significant differences in antiviral activity were detected between HCV genotypes 1b and 3 or between patients with and without compensated cirrhosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗
DOE OSTI2024

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories

Abstract The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling.

54 ENVIRONMENTAL SCIENCES↗