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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Host Onboarding Tool (HObT) v1.0.0

The Host OnBoarding Tool (Hobt) is a publicly accessible, web-based software designed to organize and share information about microbial hosts under development at the Agile BioFoundry (ABF). It streamlines the assessment, tracking, and sharing of information related to microbial host development and provides a centralized platform where users can rapidly evaluate hosts' readiness for various bio processes. HObT leverages the Tier System, a standardized host development framework that organizes and assesses microbial hosts based on their readiness for biomanufacturing. Each tier outlines key targets—including genetic tools, growth conditions, omics data, and predictive models—needed to transform new or emerging microbes into established production platforms. By applying clear criteria for advancement, the Tier System helps users quickly evaluate each organism's current development status, identify gaps in available knowledge or tools, and prioritize future strain improvement efforts. Through its user-friendly interface, HObT encourages contributions of new data and insights from researchers, fostering collaboration and accelerating host development. By providing structured guidance for microbial strain advancement, HObT and the Tier System support more systematic, rapid, and cost-effective development of non-traditional microbial hosts, ultimately enhancing the efficiency and impact of biomanufacturing research and applications.

Plahar, Hector [Lawrence Berkeley National Laborat↗
DOE OSTI2021

Rhoptry kinase protein 39 (ROP39) is a novel factor that recruits host mitochondria to the parasitophorous vacuole of Toxoplasma gondii

ABSTRACT Most intracellular pathogens replicate in a vacuole to avoid the defense system of the host. A few pathogens recruit host mitochondria around those vacuoles, but the molecules responsible for mitochondrial recruitment remain unidentified. It is only in the apicomplexan parasite Toxoplasma gondii, that mitochondrial association factor 1b (MAF1b) has been identified as an association factor for host mitochondria. Here, we show that rhoptry kinase family protein 39 (ROP39) induces host mitochondrial recruitment in T. gondii. We found that the abundance of ROP39 was increased on host mitochondria extracted from human foreskin fibroblasts (HFFs) infected with T. gondii. ROP39 expressed exogenously in HFFs localized on host mitochondria, indicating that it has the potential to bind to host mitochondria without assistance from other parasite factors. Confocal microscopy revealed that ROP39 colocalized with host mitochondria on the membrane of parasitophorous vacuoles, in which the parasites reside. Moreover, we observed about a 10% reduction in the level of mitochondrial association in rop39-knockout parasites compared with a parental strain.

Fukumoto, Junpei↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to West Nile Virus Infection, Processed Experimental Dataset Catalog

West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flavivirus) by the National Institute of Allergy and Infectious Diseases (NIAID), and are known to cause severe infections in humans where lethal host-associated mechanisms are not clearly defined. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding a specific West Nile virus [NCBITAXON:11082] (WNV-NY99 382) experimental infection study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Dependence of the Type Ia Supernova Host Bias on Observation or Fitting Technique

More luminous Type Ia supernovae prefer less massive hosts and regions of higher star formation. This correlation is inverted during width–color–luminosity light-curve standardization resulting in step-like biases of distance measurements with respect to host properties. Using the PMAS/PPak Integral-field Supernovahosts COmpilation (PISCO) supernova host sample and Sloan Digital Sky Survey, Galaxy Evolution Explorer, and Two Micron All Sky Survey photometry, we compare host stellar mass and specific star-formation rate (sSFR) from different observation methods, including local versus global, and fitting techniques to measure their impact on the host step biases. Mass-step measurements for all our mass samples are consistent within a 1σ significance from –0.03 ± 0.02 mag to –0.04 ± 0.02 mag. Including or excluding UV information had no effect on measured mass-step size or location. sSFR step sizes are more significant than mass-step measurements and varied from 0.05 ± 0.03 mag (Hα) and 0.06 ± 0.02 mag (UV) for a 51 host sample. The sSFR step location is influenced by the mass sample used to normalize star formation and by sSFR tracer choice. The step size is reduced to 0.04 ± 0.03 mag when using all available 73 hosts with Hα measurements. This 73 PISCO host subsample overall lacked a clear step signal, but here we are searching for whether different choices of mass or sSFR estimation can create a step signal. We find no evidence that different observation or fitting techniques choices can create a distance measurement step in either mass or sSFR.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Environmental Quenching of Low-surface-brightness Galaxies Near Hosts from Large Magellanic Cloud to Milky Way Mass Scales

Low-surface-brightness galaxies (LSBGs) are excellent probes of quenching and other environmental processes near massive galaxies. We study an extensive sample of LSBGs near massive hosts in the local universe that are distributed across a diverse range of environments. The LSBGs with surface-brightness ${\mu }_{\mathrm{eff},{g}}\gt 24.2\,\mathrm{mag}\,{\mathrm{arcsec}}^{-2}$ are drawn from the Dark Energy Survey Year 3 catalog while the hosts with masses $9.0\lt \mathrm{log}({{ \mathcal M }}_{\star }/{M}_{\odot })\lt 11.0$ comparable to the Milky Way and the Large Magellanic Cloud are selected from the z0MGS sample. We study the projected radial density profiles of LSBGs as a function of their color and surface brightness around hosts in both the rich Fornax–Eridanus cluster environment and the low-density field. We detect an overdensity with respect to the background density, out to 2.5 times the virial radius for both hosts in the cluster environment and the isolated field galaxies. When the LSBG sample is split by g − i color or surface brightness μ eff, g , we find the LSBGs closer to their hosts are significantly redder and brighter, like their high-surface-brightness counterparts. The LSBGs form a clear “red sequence” in both the cluster and isolated environments that is visible beyond the virial radius of the hosts. This suggests preprocessing of infalling LSBGs and a quenched backsplash population around both host samples. More so, the relative prominence of the “blue cloud” feature implies that preprocessing is ongoing near the isolated hosts compared to the cluster environment where the LSBGs are already well processed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2013

The Host Galaxies of Type Ia Supernovae Discovered by the Palomar Transient Factory

We present spectroscopic observations of the host galaxies of 82 low-redshift type Ia supernovae (SNe Ia) discovered by the Palomar Transient Factory (PTF). We determine star-formation rates, gas-phase stellar metallicities, and stellar masses and ages of these objects. As expected, strong correlations between the SN Ia light-curve width (stretch) and the host age mass metallicity are found: fainter, faster-declining events tend to be hosted by older massive metal-rich galaxies. There is some evidence that redder SNe Ia explode in higher metallicity galaxies, but we found no relation between the SN colour and host galaxy extinction based on the Balmer decrement, suggesting that the colour variation of these SNe does not primarily arise from this source. SNe Ia in higher-mass metallicity galaxies also appear brighter after stretch colour corrections than their counterparts in lower mass hosts, and the stronger correlation is with gas-phase metallicity suggesting this may be the more important variable. We also compared the host stellar mass distribution to that in galaxy targeted SN surveys and the high-redshift untargeted Supernova Legacy Survey (SNLS). SNLS has many more low mass galaxies, while the targeted searches have fewer. This can be explained by an evolution in the galaxy stellar mass function, coupled with a SN delay-time distribution proportional to t1. Finally, we found no significant difference in the mass--metallicity relation of our SN Ia hosts compared to field galaxies, suggesting any metallicity effect on the SN Ia rate is small.

host↗
NASA NTRS2022

Asparagine Biosynthesis as a Mechanism of Increased Host Lethality Induced by Serratia Marcescens in Simulated Microgravity Environments

While studies have shown an increase in pathogenicity in several microbes during spaceflight and after exposure to simulated microgravity, the mechanisms underlying these changes in phenotype are not understood across different pathogens, particularly in opportunistic pathogens. This study evaluates the mechanism for increased virulence of the opportunistic gram-negative bacterium, Serratia marcescens, in simulated microgravity. Low-shear modeled microgravity (LSMMG) is used in ground-based studies to simulate the effects of microgravity as experienced in spaceflight. Our previous findings showed that there was a significant increase in mortality rates of the Drosophila melanogaster host when infected with either spaceflight or LSMMG treated S. marcescens. Here, we report that LSMMG increases asparagine uptake and synthesis in S. marcescens and that the increased host lethality induced by LSMMG bacteria grown in rich media can be recapitulated in minimal media by adding only aspartate and glutamine, the substrates of asparagine biosynthesis. Interestingly, increased bacterial growth rate alone is not sufficient to contribute to maximal host lethality, since the addition of aspartate to minimal media caused an LSMMG-specific increase in bacterial growth rate that is comparable to that induced by the combination of aspartate and glutamine, but this increase in growth does not cause an equivalent rate of host mortality. However, the addition of both aspartate and glutamine cause both an increase in host mortality and an overexpression of asparagine pathway genes in a LSMMG-dependent manner. We also report that L-asparaginase-mediated breakdown of asparagine is an effective countermeasure for the increased host mortality caused by LSMMG-treated bacteria. This investigation underscores the importance of the asparagine utilization pathway by helping uncover molecular mechanisms that underlie increased mortality rates of a model host infected with microgravity-treated S.marcescens and provides a potential mitigation strategy.

simulated microgravity↗
DOE OSTI2025

GA-NIFS and EIGER: A merging quasar host at z = 7 with an overmassive black hole

The James Webb Space Telescope is revolutionising our ability to understand the host galaxies and local environments of high-z quasars. Here we obtain a comprehensive understanding of the host galaxy of the z = 7.08 quasar J1120+0641 by combining NIRSpec integral field spectroscopy with NIRCam photometry of the host continuum emission. Our emission-line maps reveal that this quasar host is undergoing a merger with a bright companion galaxy. The quasar host and the companion have similar dynamical masses of ∼10 10 M ⊙ , suggesting that this is a major galaxy interaction. Through detailed quasar subtraction and SED fitting using the NIRCam data, we obtained an estimate of the host stellar mass of M ∗ = (3.0 −1.4 +2.5 ) × 10 9 M ⊙ , with M ∗ = (2.7 −0.5 +0.5 ) × 10 9 M ⊙ for the companion galaxy. Using the Hβ Balmer line, we estimated a virial black hole mass of M BH = (1.9 −1.1 +2.9 ) × 109 M ⊙ . Thus, J1120+0641 has an extreme black hole–stellar mass ratio of M BH /M ∗ = 0.63 −0.31 +0.54 , which is ∼3 dex larger than expected by the local scaling relations between black hole and stellar mass. J1120+0641 is powered by an overmassive black hole with the highest reported black hole–stellar mass ratio in a quasar host that is currently undergoing a major merger. These new insights highlight the power of JWST for measuring and understanding these extreme first quasars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

The host galaxies of 106 rapidly evolving transients discovered by the Dark Energy Survey

Rapidly evolving transients (RETs), also termed fast blue optical transients, are a recently discovered group of astrophysical events that display rapid luminosity evolution. RETs typically rise to peak in less than 10 d and fade within 30, a time-scale unlikely to be compatible with the decay of Nickel-56 that drives conventional supernovae (SNe). Their peak luminosity spans a range of -15 < Mg < -22.5, with some events observed at redshifts greater than 1. Their evolution on fast time-scales has hindered high-quality follow-up observations, and thus their origin and explosion/emission mechanism remains unexplained. In this paper, we present the largest sample of RETs to date, comprising 106 objects discovered by the Dark Energy Survey, and perform the most comprehensive analysis of RET host galaxies. Using deep-stacked photometry and emission lines from OzDES spectroscopy, we derive stellar masses and star formation rates (SFRs) for 49 host galaxies, and metallicities ([O/H]) for 37. Here, we find that RETs explode exclusively in star-forming galaxies and are thus likely associated with massive stars. Comparing RET hosts to samples of host galaxies of other explosive transients as well as field galaxies, we find that RETs prefer galaxies with high specific SFRs ($\langle$log(sSFR)$\rangle$ ~ -9.6), indicating a link to young stellar populations, similar to stripped-envelope SNe. RET hosts appear to show a lack of chemical enrichment, their metallicities akin to long-duration gamma-ray bursts and superluminous SN host galaxies ($\langle$12+ log (O/H)$\rangle$ ~ 9.4). There are no clear relationships between mass or SFR of the host galaxies and the peak magnitudes or decline rates of the transients themselves.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Subhaloes are anisotropically distributed and aligned with the smooth matter distribution of their host haloes

ABSTRACT We investigate the distributions of subhaloes about their hosts in two suites of zoom-in N-body simulations of halo growth – one suite focused on Milky Way-Mass haloes ($\sim 10^{12} \, \mathrm{M}_{\odot }$) and another focused on cluster-mass haloes ($\sim 10^{15} \, \mathrm{M}_{\odot }$) in the Symphony simulation suite. We find, in agreement with previous work on this subject, that subhaloes are distributed anisotropically about their host haloes. In particular, the positions of subhaloes lie preferentially near the major axes of their host haloes, possibly implying that satellite galaxies will exhibit a similar alignment. Furthermore, we show that in two-dimensional projection subhaloes are more likely to be observed near the halo centre (where the central galaxy presumably resides) when the host halo is projected nearly along its major axis. This projection effect is significant. Within projected radii of a few per cent of the virial radius of the host halo, the fraction of mass in subhaloes is $\sim 175~{{\ \rm per\ cent}}$ larger for Milky Way-mass haloes and as much as $\sim 195~{{\ \rm per\ cent}}$ larger for cluster haloes when projected along the major axis as compared to the average from a random projection. This result has consequences for many applications including the interpretation of gravitational lenses. Finally, we find that the orbital angular momentum vector of subhaloes is aligned with the angular momentum vector of their host halo, indicating that a significant component of a halo’s angular momentum may be carried in its subhaloes. This has consequences for galaxy formation models which use host halo angular momentum as a proxy for galaxy momentum.

Mezini, Lorena (ORCID:0000000300053973)↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

AXI4MLIR: User-Driven Automatic Host Code Generation for Custom AXI-Based Accelerators

Tensor algebra operations represent an important class of algorithms used across many applications, including machine learning, scientific computing, and data analytics. As a result, the efficient generation of custom accelerators for tensor operations has received increased attention. Previous efforts have produced automated tools enabling users to prototype and explore optimized accelerators. However, little effort has been focused on the host-accelerator interaction in these tools. Efficient use of hardware accelerators requires knowledge about the accelerator's capabilities (operations, data formats, and opcode support), the host CPU microarchitecture (e.g., memory hierarchy), the host-accelerator interface, and the application's features (which code regions should be mapped onto an accelerator). Manually rewriting the original applications to facilitate improved custom accelerator mapping is an error-prone and time-consuming endeavor. To cope with this, we propose AXI4MLIR, a new framework to automatically generate and optimize the communication between the host CPU and arbitrary accelerators that implement linear algebra algorithms. AXI4MLIR extends the MLIR compiler framework to automatically generate efficient host-accelerator driver code for accelerators with AXI-based interfaces. Our compiler extensions enable automatic driver code generation while carefully considering the host's memory hierarchy and target accelerator features. To demonstrate the flexibility and utility of AXI4MLIR, we test it with diverse use cases that include different types of accelerators, tiling scenarios, and dataflow schemes. We compare our experimental results to manual implementations of host-accelerator driver code and find that our approach can reduce CPU cache references by 56% and deliver up to a 1.65x speedup.

Bohm Agostini, Nicolas↗
DOE OSTI2024

Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.

ABSTRACT The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia , the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii , a newly described microsporidian parasite of Daphnia . We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina , as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia–O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCE The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii . Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Interferon-Stimulated Response to Virus Infection, Processed Experimental Dataset Catalog

Human Interferon (IFN) alpha, beta, and gamma participate in the body's natural immune response to lethal virus infection and disease.The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Human Interferon (IFN), interferon alpha (IFNα), interferon beta (IFNβ), and/or interferon gamma (IFNγ) stimulated response to an experimental virus infection treatment study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets

Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.

Immunology↗
DOE OSTI2025

StreamGen: Connecting Populations of Streams and Shells to Their Host Galaxies

In this work, we study how the abundance and dynamics of populations of disrupting satellite galaxies change systematically as a function of host galaxy properties. We apply a theoretical model of the phase-mixing process to classify intact satellite galaxies and stellar streamlike and shell-like debris in ∼1500 Milky Way–mass systems generated by a semi-analytic galaxy formation code, SatGen. In particular, we test the effect of host galaxy halo mass, disk mass, ratio of disk scale height to length, and stellar feedback model on disrupting satellite populations. We find that the counts of tidal debris are consistent across all host galaxy models, within a given host mass range, and that all models can have streamlike debris on low-energy orbits, consistent with that observed around the Milky Way. However, we find a preference for streamlike debris on lower-energy orbits in models with a thicker (lower-density) host disk or on higher-energy orbits in models with a more massive host disk. Importantly, we observe significant halo-to-halo variance across all models. These results highlight the importance of simulating and observing large samples of Milky Way–mass galaxies and accounting for variations in host properties when using disrupting satellites in studies of near-field cosmology.

dark matter↗