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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Developing multi-gene CRISPRa/i programs to accelerate DBTL cycles in ABF hosts engineered for chemical production

This project developed and implemented a modular CRISPR activation and interference (CRISPRa/i) platform to accelerate strain optimization and pathway development for industrially relevant microbial hosts. By integrating multiplexed transcriptional perturbation tools with data-driven Design–Build–Test–Learn (DBTL) workflows, the team achieved reductions in cycle time and enhanced production of industrial aromatics, particularly 4-aminocinnamic acid (4-ACA), in Pseudomonas putida. Key accomplishments included: ● Development of a robust, tunable CRISPRa/i system in P. putida that enabled efficient multi-target gene regulation via guide RNA (gRNA) programs ● Completion of two full DBTL cycles, guided by machine learning (ML) models trained on transcriptomic and performance data, reducing engineering time by over 30% ● Optimization of multi-gene regulatory programs to balance expression of host and pathway modules, improve 4-ACA titers, and resolve metabolic bottlenecks ● Demonstration of system portability through a limited proof-of-concept extension in Acinetobacter baylyi, underscoring the generalizability of the approach ● Evaluation of strain performance on lignocellulosic biomass-derived substrates, demonstrating the feasibility of converting renewable carbon into aromatic building blocks These results illustrate the feasibility of applying ML-guided CRISPRa/i perturbation strategies to accelerate strain development in complex microbial systems. The resulting tools and datasets contribute to DOE objectives by improving platform predictability, reducing development costs, and enabling broader access to sustainable, economically viable bioproduction technologies.

09 BIOMASS FUELS↗
DOE OSTI2023

Hi-C Viral Host Links

Hi-C Viral Host Links: virus-host associations indicated by Hi-C sequencing were processed by Phase Genomics by folowing the protocal, https://www.biorxiv.org/content/10.1101/2021.06.14.448389v1.full

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Corynebacterium glutamicum as an Efficient Omnivorous Microbial Host for the Bioconversion of Lignocellulosic Biomass

Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, 13 C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum . 13 C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. 13 C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.

13C-fingerprinting↗
DOE OSTI2024

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of equine mares as reservoir hosts for pathogenic species of Leptospira

Equine leptospirosis can result in abortion, stillbirth, neonatal death, placentitis, and uveitis. Horses can also act as subclinical reservoir hosts of infection, which are characterized as asymptomatic carriers that persistently excrete leptospires and transmit disease. In this study, PCR and culture were used to assess urinary shedding of pathogenic Leptospira from 37 asymptomatic mares. Three asymptomatic mares, designated as H2, H8, and H9, were PCR-positive for lipL32, a gene specific for pathogenic species of Leptospira. One asymptomatic mare, H9, was culture-positive, and the recovered isolate was classified as L. kirschneri serogroup Australis serovar Rushan. DNA capture and enrichment of Leptospira genomic DNA from PCR-positive, culture-negative samples determined that asymptomatic mare H8 was also shedding L. kirschneri serogroup Australis, whereas asymptomatic mare H2 was shedding L. interrogans serogroup Icterohaemorrhagiae. Sera from all asymptomatic mares were tested by the microscopic agglutination test (MAT) and 35 of 37 (94.6%) were seropositive with titers ranging from 1:100 to 1:3200. In contrast to asymptomatic mares, mare H44 presented with acute spontaneous abortion and a serum MAT titer of 1:102,400 to L. interrogans serogroup Pomona serovar Pomona. Comparison of L. kirschneri serogroup Australis strain H9 with that of L. interrogans serogroup Pomona strain H44 in the hamster model of leptospirosis corroborated differences in virulence of strains. Since lipopolysaccharide (LPS) is a protective antigen in bacterin vaccines, the LPS of strain H9 (associated with subclinical carriage) was compared with strain H44 (associated with spontaneous abortion). This revealed different LPS profiles and immunoreactivity with reference antisera. It is essential to know what species and serovars of Leptospira are circulating in equine populations to design efficacious vaccines and diagnostic tests. Our results demonstrate that horses in the US can act as reservoir hosts of leptospirosis and shed diverse pathogenic Leptospira species via urine. This report also details the detection of L. kirschneri serogroup Australis serovar Rushan, a species and serotype of Leptospira, not previously reported in the US.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism

Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.

Microbiology↗
DOE OSTI2021

Differential Accumulation of Misfolded Prion Strains in Natural Hosts of Prion Diseases

Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of neurodegenerative protein misfolding diseases that invariably cause death. TSEs occur when the endogenous cellular prion protein (PrP C ) misfolds to form the pathological prion protein (PrP Sc ), which templates further conversion of PrP C to PrP Sc , accumulates, and initiates a cascade of pathologic processes in cells and tissues. Different strains of prion disease within a species are thought to arise from the differential misfolding of the prion protein and have different clinical phenotypes. Different strains of prion disease may also result in differential accumulation of PrP Sc in brain regions and tissues of natural hosts. Here, we review differential accumulation that occurs in the retinal ganglion cells, cerebellar cortex and white matter, and plexuses of the enteric nervous system in cattle with bovine spongiform encephalopathy, sheep and goats with scrapie, cervids with chronic wasting disease, and humans with prion diseases. By characterizing TSEs in their natural host, we can better understand the pathogenesis of different prion strains. This information is valuable in the pursuit of evaluating and discovering potential biomarkers and therapeutics for prion diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geogenic, Anthropogenic, and Authigenic Minerals Hosting Arsenic and Antimony in Yellowknife Bay Sediments

Abstract Yellowknife Bay (Great Slave Lake, Northwest Territories, Canada) is a water body valued by surrounding communities for its subsistence, recreational, and cultural use. Located directly downstream of the former Giant Mine and Con Mine, Yellowknife Bay has received inputs from mine waste streams enriched in arsenic (As), antimony (Sb), and metals since the late 1930s. Lake sediments in Yellowknife Bay provide a record of metal(loid) contamination from aerially deposited roaster stack emissions, mine effluent, and Giant Mine tailings. A sediment sampling program was conducted in Yellowknife Bay to characterize As and Sb mineralogy using scanning electron microscopy-mineral liberation analysis. Mineralogical analysis of As- and Sb-hosted minerals in nine sediment cores suggests that arsenic trioxide (As2O3), originally deposited during the period of peak-mining emissions, has since been transformed into authigenic sulfides (interpreted to be realgar) down core from peak-mining emissions. Arsenic has also been attenuated by iron (Fe)-oxyhydroxides and roaster-generated iron oxides up-core from peak-mining emissions, near the sediment–water interface. The Sb-bearing minerals appear to be stable in Yellowknife Bay sediments, with no conclusive evidence of post-depositional mobility having been identified. The observed prevalence of arsenic trioxide in surface sediments proximal to Giant Mine suggests that As and Sb contamination is ongoing, likely from terrestrial weathering of contaminated soils and shoreline outcrops. Arsenic-bearing oxide minerals prevalent in surface sediments may become unstable should redox conditions in the hypolimnion change; prolonged anoxia could destabilize the As hosting minerals and release As to bottom waters. Therefore, long-term monitoring of the water column, including hypolimnion conditions, in Yellowknife Bay is recommended.

Mineralogy↗
DOE OSTI2020

A Likely Magnetic Activity Cycle for the Exoplanet Host M Dwarf GJ 3512

Current radial velocity data from specialized instruments contain a large amount of information that may pass unnoticed if their analysis is not accurate. The joint use of Bayesian inference tools and frequency analysis has been shown as effective in revealing exoplanets but they have been used less frequently to investigate stellar activity. We intend to use radial velocity data of the exoplanet host star GJ 3512 to investigate its magnetic activity. Our study includes the analysis of the photometric data available. The main objectives of our work are to constrain the orbital parameters of the exoplanets in the system, to determine the current level of activity of the star and to derive an activity cycle length for it. An adaptive importance sampling method was used to determine the parameters of the exoplanets orbit. Generalized Lomb–Scargle periodograms were constructed with both radial velocity curve and photometric data. A careful analysis of the harmonic frequencies was conducted in each periodogram. Our fit to multiple Keplerian orbits constrained the orbital parameters of two giant gas planets orbiting the star GJ 3512. The host star showed an increase of its magnetic activity during the last observing campaign. The accurate fit of the radial velocity curve data to the multi-Keplerian orbit permitted to reveal the star rotation in the residuals of the best fit and estimate an activity cycle length of ~14 yr.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

The Chemical Inventory of the Planet-hosting Disk PDS 70

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS 70 disk and report the first chemical inventory of the system. With a spatial resolution of 0."4–0."5 (~50 au), 12 species are detected, including CO isotopologs and formaldehyde, small hydrocarbons, HCN and HCO{sup +} isotopologs, and S-bearing molecules. SO and CH{sub 3}OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub)millimeter continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature, and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the nondetections. Excitation temperature is obtained for H{sub 2}CO. Deuteration and nitrogen fractionation profiles from the hydrocyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon-to-oxygen ratio C/O > 1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

The High-energy Spectrum of the Nearby Planet-hosting Inactive Mid-M Dwarf LHS 3844

To fully characterize the atmospheres, or lack thereof, of terrestrial exoplanets, we must include the high-energy environments provided by their host stars. The nearby mid-M dwarf LHS 3844 hosts a terrestrial world that lacks a substantial atmosphere. We present a time-series UV spectrum of LHS 3844 from 1131 to 3215 Å captured by HST/COS. We detect one flare in the FUV that has an absolute energy of 8.96 ± 0.77 × 10{sup 28} erg and an equivalent duration of 355 ± 31 s. We extract the flare and quiescent UV spectra separately. For each spectrum, we estimate the Lyα flux using correlations between UV line strengths. We use Swift-XRT to place an upper limit on the soft X-ray flux and construct a differential emission model to estimate flux that is obscured by the interstellar medium. We compare the differential emission model flux estimates in the XUV to other methods that rely on scaling from the Lyα, Si iv, and N v lines in the UV. The XUV, FUV, and NUV flux of LHS 3844 relative to its bolometric luminosity is log{sub 10}(L {sub band}/L {sub Bol}) =−3.65, −4.16, and −4.48, respectively, for the quiescent state. These values agree with trends in high-energy flux as a function of stellar effective temperature found by the MUSCLES survey for a sample of early-M dwarfs. Many of the most spectroscopically accessible terrestrial exoplanets orbit inactive mid-to-late M dwarfs like LHS 3844. Measurements of M dwarf high-energy spectra are preferable for exoplanet characterization but are not always possible. The spectrum of LHS 3844 is a useful proxy for the current radiation environment for these worlds.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

TOI-532b: The Habitable-zone Planet Finder confirms a Large Super Neptune in the Neptune Desert orbiting a metal-rich M-dwarf host

We confirm the planetary nature of TOI-532b, using a combination of precise near-infrared radial velocities with the Habitable-zone Planet Finder, Transiting Exoplanet Survey Satellite (TESS) light curves, ground-based photometric follow up, and high-contrast imaging. TOI-532 is a faint (J ~ 11.5) metal-rich M dwarf with T{sub eff} = 3957 ± 69 K and [Fe/H] = 0.38 ± 0.04; it hosts a transiting gaseous planet with a period of ~2.3 days. Joint fitting of the radial velocities with the TESS and ground-based transits reveal a planet with radius of 5.82 ± 0.19 R {sub ⊕}, and a mass of 61.5{sub -9.3}{sup +9.7} M {sub ⊕}. TOI-532b is the largest and most massive super Neptune detected around an M dwarf with both mass and radius measurements, and it bridges the gap between the Neptune-sized planets and the heavier Jovian planets known to orbit M dwarfs. It also follows the previously noted trend between gas giants and host-star metallicity for M-dwarf planets. In addition, it is situated at the edge of the Neptune desert in the Radius–Insolation plane, helping place constraints on the mechanisms responsible for sculpting this region of planetary parameter space.

36 MATERIALS SCIENCE↗
DOE OSTI2021

It’s Dust: Solving the Mysteries of the Intrinsic Scatter and Host-galaxy Dependence of Standardized Type Ia Supernova Brightnesses

The use of Type Ia supernovae (SNe Ia) as cosmological tools has motivated significant effort to understand what drives the intrinsic scatter of SN Ia distance modulus residuals after standardization, characterize the distribution of SN Ia colors, and explain why properties of the host galaxies of the SNe correlate with SN Ia distance modulus residuals. We use a compiled sample of ~1450 spectroscopically confirmed photometric light curves of SNe Ia and propose a solution to these three problems simultaneously that also explains an empirical 11 σ detection of the dependence of Hubble residual scatter on SN Ia color. We introduce a physical model of color where intrinsic SN Ia colors with a relatively weak correlation with luminosity are combined with extrinsic dust-like colors ( E ( B - V )) with a wide range of extinction parameter values ( R V ). This model captures the observed trends of Hubble residual scatter and indicates that the dominant component of SN Ia intrinsic scatter is variation in R V . We also find that the recovered E ( B - V ) and R V distributions differ based on global host-galaxy stellar mass, and this explains the observed correlation ( γ ) between mass and Hubble residuals seen in past analyses, as well as an observed 4.5 σ dependence of γ on SN Ia color. This finding removes any need to ascribe different intrinsic luminosities to different progenitor systems. Finally, we measure biases in the equation of state of dark energy ( w ) up to |Δ w | = 0.04 by replacing previous models of SN color with our dust-based model; this bias is larger than any systematic uncertainty in previous SN Ia cosmological analyses.

Astronomy & Astrophysics↗
DOE OSTI2023

Does Feedback from Supermassive Black Holes Coevolve with the Host in Type 2 Quasars?

The feedback from the accretion of central supermassive black holes (SMBHs) is a hot topic in the coevolution of SMBHs and their host galaxies. By tracing the large-scale outflow using the line profile and bulk velocity shift of [O III ]λ5007, the evolutionary role of outflow is studied here on a large sample of 221 type 2 quasars (QSO2s) extracted from Reyes et al. By following our previous study on local Seyfert 2 galaxies, the current spectral analysis on the Sloan Digital Sky Survey spectroscopic database enables us to arrive at the following results: (1) by using the Lick indices, we confirm that QSO2s are, on average, more frequently associated with younger stellar populations than Seyfert galaxies; (2) QSO2s with a stronger outflow tend to be associated with a younger stellar population, which implies a coevolution between the feedback from SMBHs and the host in QSO2s; (3) although occupied at the high L bol /L Edd end, the QSO2s follow the L bol /L Edd -D n (4000) sequence established from local, less-luminous Seyfert galaxies, which suggests a decrease of the accretion activity of SMBHs and also of feedback as the circumnuclear stellar population continuously ages.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

First Impressions: Early-time Classification of Supernovae Using Host-galaxy Information and Shallow Learning

Substantial effort has been devoted to the characterization of transient phenomena from photometric information. Automated approaches to this problem have taken advantage of complete phase coverage of an event, limiting their use for triggering rapid follow-up of ongoing phenomena. In this work, we introduce a neural network with a single recurrent layer designed explicitly for early photometric classification of supernovae (SNe). Our algorithm leverages transfer learning to account for model misspecification, host-galaxy photometry to solve the data-scarcity problem soon after discovery, and a custom weighted loss to prioritize accurate early classification. We first train our algorithm using state-of-the-art transient and host-galaxy simulations, then adapt its weights and validate it on the spectroscopically confirmed SNe Ia, SNe II, and SNe Ib/c from the Zwicky Transient Facility Bright Transient Survey. On observed data, our method achieves an overall accuracy of 82% ± 2% within 3 days of an event’s discovery, and an accuracy of 87% ± 5% within 30 days of discovery. At both early and late phases, our method achieves comparable or superior results to the leading classification algorithms with a simpler network architecture. These results help pave the way for rapid photometric and spectroscopic follow-up of scientifically valuable transients discovered in massive synoptic surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Modeling supercritical CO 2 flow and mineralization in reactive host rocks with PFLOTRAN v7.0

Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

Critical Minerals↗
DOE OSTI2020

Host cells and methods for producing isopentenol from mevalonate

The present invention provides for a genetically modified host cell capable of producing isopentenol and/or 3-methyl-3-butenol, comprising (a) an increased expression of phosphomevalonate decarboxylase (PMD) (b) an increased expression of a phosphatase capable of converting isopentenol into 3-methyl-3-butenol, (c) optionally the genetically modified host cell does not express, or has a decreased expression of one or more of NudB, phosphomevalonate kinase (PMK), and/or PMD, and (d) optionally one or more further enzymes capable of converting isopentenol and/or 3-methyl-3-butenol into a third compound, such as isoprene.

Lee, Taek Soon↗
DOE OSTI2021

Host cell modified to produce lactams

The present invention provides for a genetically modified host cell capable of producing a lactam comprising a 2-pyrrolidone synthase, or an enzymatically active fragment thereof, heterologous to the host cell.

Zhang, Jingwei↗