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Results for “Partial Replication”

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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Hanford low-activity waste glass composition-temperature-melt viscosity relationships

This study developed a model for predicting viscosity of alkali-alumino-borosilicate glass melts as functions of composition and temperature. The model is based on a total of 3935 viscosity-temperature data from 574 glasses with viscosity values ranging from 2.53 to 7260 Poise (P) in the temperature range of 900–1260°C. Several different model forms were surveyed, including those based on Arrhenius, Vogel-Fulcher-Tammann, Avramov-Milchev, and Mauro-Yue-Ellison-Gupta-Allen. For each of these models, combinations of the temperature-independent parameters were fitted to composition. It was found that generally fitting more than one temperature-independent parameter as functions of composition resulted in overfitting. The Avramov-Milchev-based model was found to best represent the Hanford low-activity waste glass melt viscosity data based on model fit and validation statistics. A 21-term partial quadratic mixture model was recommended for use. This model predicts melt viscosity with a root-mean square error of .1736 ln(P), which is similar to the error in viscosity measurements from replicate glass analyses of .1383 ln(P). Viscosity was found to be most increased by SiO 2 > Al 2 O 3 > ZrO 2 > SnO 2 and most decreased by Li 2 O > Na 2 O > B 2 O 3 > CaO > K 2 O > MgO, at temperatures from 900 to 1260°C.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Matrix multiplication operations using pair-wise load and splat operations

Mechanisms for performing a matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A pair-wise load and splat operation is performed to load a pair of scalar values of a second vector operand and replicate the pair of scalar values within a second target vector register. An operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored. This operation may be repeated for a second pair of scalar values of the second vector operand.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Structural studies of viperin, an antiviral radical SAM enzyme

Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45–362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45–74) and a partially ordered C-terminal extension (residues 285–362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. As a result, the viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SPUS-Small-PDE-U-net-Solver

Small PDE U-Net Solver (SPUS) is a compact and efficient foundation model (FM) designed as a unified neural operator for solving a wide range of partial differentialequations (PDEs). SPUS leverages a lightweight residual U-Net-based architecture as a foundation model architecture. To enable effective learning in this minimalist framework, SPUS utilizes a simple yet powerful auto-regressive pretraining strategy which closely replicates the behavior of numerical solvers to learn the underlying physics. SPUS is designed to be pretrained on a diverse set of fluid dynamics PDEs from public benchmark datasets.

Siddik, Abu↗
DOE OSTI2017

Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis

ABSTRACT Coronaviruses (CoVs) encode a mixture of highly conserved and novel genes, as well as genetic elements necessary for infection and pathogenesis, raising the possibility of common targets for attenuation and therapeutic design. In this study, we focused on highly conserved nonstructural protein 16 (NSP16), a viral 2' O -methyltransferase (2' O -MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of Middle East respiratory syndrome CoV (MERS-CoV) NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2' O -MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo . Further examination indicated that dNSP16 mutant MERS-CoV had a type I interferon (IFN)-based attenuation and was partially restored in the absence of molecules of IFN-induced proteins with tetratricopeptide repeats. Importantly, the robust attenuation permitted the use of dNSP16 mutant MERS-CoV as a live attenuated vaccine platform protecting from a challenge with a mouse-adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2' O -MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting. IMPORTANCE Coronavirus (CoV) emergence in both humans and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of severe acute respiratory syndrome CoV (SARS-CoV), MERS-CoV, porcine epidemic diarrhea virus, and swine delta CoV in the 21st century. These studies describe an approach that effectively targets the highly conserved 2' O -MTase activity of CoVs for attenuation. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-CoV functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2' O -MTase function across CoVs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Using Artificial Soiling to Rank Anti-Soiling Coatings for Arid Climates

A simple method to evaluate (e.g., screen and rank) the performance of coatings that are fully or partially anti-soiling (AS) is lacking within the PV industry. Artificial soiling may be used as a rapid and economical assessment approach, offering an efficient alternative to time-intensive, site-specific field testing. In this study, we present an artificial soiling method to replicate the anti-soiling performance rankings of two groups of coated glass samples supplied by two manufacturers (group C with CA, CP, and CS coatings; group A with AC coating). These are compared to field aging in two climates: semi-arid Lemoore, California over 4 months, and the hot desert in Mesa, Arizona over 7 months. Both field and indoor performance ranking utilize the transmittance ratio, defined as the optical transmittance between a coated sample and an uncoated reference in each group, as an evaluation metric to assess the effectiveness of the artificial soiling approach in replicating field soiling. It is critical to mimic the dominant field meteorological conditions associated with soiling-prone days and vulnerable times of day during the soiling season. Our results reveal that the use of artificial soiling for field performance ranking among coatings strongly depends on the soil type (composition and particle distribution), dust surface density, and prevalent environmental factors (wetting saturation by humidity, dew condensation extent, and prior weathering history of the coating). The similar rank order relative to the field suggests that the artificial soiling approach presented may be used for down-selecting anti-soiling coatings prior to prolonged field validation.

14 SOLAR ENERGY↗
DOE OSTI2017

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. Furthermore, the striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Direct Numerical Simulation of Partial Fuel Stratification Assisted Lean Premixed Combustion for Assessment of Hybrid G-Equation/Well-Stirred Reactor Model

Partial fuel stratification (PFS) is a promising fuel injection strategy to stabilize lean premixed combustion in spark-ignition (SI) engines. PFS creates a locally stratified mixture by injecting a fraction of the fuel, just before spark timing, into the engine cylinder containing homogeneous lean fuel/air mixture. Further, this locally stratified mixture, when ignited, results in complex flame structure and propagation modes similar to partially premixed flames and allows for faster and more stable flame propagation than a homogeneous lean mixture. This study focuses on understanding the detailed flame structures associated with PFS-assisted lean premixed combustion. First, a two-dimensional direct numerical simulation (DNS) is performed using detailed fuel chemistry, experimental pressure trace, and realistic initial conditions mapped from a prior engine large-eddy simulation (LES), replicating practical lean SI operating conditions. DNS results suggest that the conventional triple flame structure is prevalent during the initial stage of flame kernel growth. Both premixed and nonpremixed combustion modes are present with the premixed mode contributing dominantly to the total heat release. Detailed analysis further reveals the effects of flame stretch and fuel pyrolysis on flame displacement speed. Based on the DNS findings, the accuracy of a hybrid G-equation/well-stirred reactor (WSR) combustion model is assessed for the PFS-assisted lean operation in the LES context. It is found that the G-equation model qualitatively captures the premixed branches of the triple flame, while the WSR model predicts the nonpremixed branch of the triple flame. Finally, potential needs for improvements to the hybrid G-equation/WSR modeling approach are discussed.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2017

Modeling and Analysis of Coupled Flow Through Packed Beds as a Diagnostic Tool for Packed Bed Reactor Health - 17172

The US Department of Energy, Office of River Protection, is building the Waste Treatment and Immobilization Plant (WTP) in Richland, Washington, to immobilize the hundreds of millions of liters of radioactive waste stored at the Hanford Site in Washington state. The offgas generated during vitrification of these wastes requires treatment to remove and/or destroy chemical and radioactive hazardous components before release to the atmosphere. In particular, volatile and semi-volatile hydrocarbon components are to be catalytically oxidized to carbon dioxide and water, whereas nitrogen oxides (NOx) are to be catalytically reduced to nitrogen and water. These tasks are accomplished in a series of packed bed reactors. Achieving the requisite Destruction/Removal Efficiency (DRE) for each of the tracked components is highly dependent on the flow characteristics of the offgas through the packed beds. The flow kinetics may be monitored and characterized during the initial warm-up of the system. The gases, initially at 76 deg. C (169 deg. F), (a) flow through one side of a countercurrent heat exchanger to recover heat from the exiting gases (which have already passed through the catalytic beds), (b) are then further heated electrically to approximately 400 deg. C (750 deg. F; the preferred operating temperature of the Thermo Catalytic Oxidizer (TCO)), (c) pass through the TCO where the reduced components of the offgas are oxidized over a supported Pt catalyst bed, (d) are partially cooled to approximately 315 deg. C (600 deg. F) by addition of approximately 25% (by weight) diluted ammonia/air mixture, (e) pass through the Selective Catalytic Reducer (SCR) where the NOx components are converted to N{sub 2} and H{sub 2}O over a supported V2O{sub 5}/TiO{sub 2} catalyst bed, and (f) exit through the hot side of the countercurrent heat exchanger. The electrical heater is not powerful enough to raise the temperature of the offgas to the desired 400 deg. C without the contribution of the heat recovered in the heat exchanger. Moreover, the thermal mass of the beds and housings of the TCO and SCR require a significant input of thermal energy to reach the desired operating temperatures; the better part of a day is required to bring the unit from ambient temperatures to operating temperatures. Therefore, the temperature of the stream during the initial warm-up of the system at each point in the system is dependent upon the thermal mass, flow dispersion, and permeability of the components, quantified as characteristic/representative volumes and residence times. By monitoring the temperature of the offgas as it enters and exits each portion of the system during this warm-up period one may model the system as a series of small Continuously Stirred Tank Reactors (CSTR)s (referred to as 'CSTRlets') to explain the flow kinetics through the catalyst beds. These component CSTRlets are adjustable in size and number, that one may model the flow profile of the gases through the catalyst beds. For example, a single large CSTR will present an effluent temperature profile with a simple exponential decay shape. Concatenating more CSTRlets generate more complex sigmoidal responses. Concatenating one CSTRlet significantly larger than the others in the train also alters the shape of the effluent temperature profile, in a fashion not replicable by a train of equal-sized CSTRlets. The ultimate goal is to accurately emulate the entire system as a representative CSTRlet train. Once accomplished, this characterization may be used in subsequent warm-ups (following shutdown for catalyst maintenance, for example) or by an intentional step change in inlet offgas temperature to detect/diagnose anomalies in flow through the beds (e.g., channeling or partial blockage.) This work presents development of this model through analytical, calculational, and empirical means. - The analytic model is accomplished by Laplace transform analysis of each component to recover component process transfer functions. - The calculational portion is performed via brute force finite element calculation. - Fitting empirical data from the warm-up of the TCO skid allows one to select the hypothetical CSTRlet trains which best fit the TCO and SCR beds for the analytical and finite element calculations. The first portion of this paper presents the development of the analytical (Laplace space) model of the coupled system. Estimated values for the initial temperature, mass, specific heat, electrical heat, and relative quantities of the offgas, catalyst beds, stainless steel housings, and ammonia dilution stream are used to generate expected temperature profiles at several selected junctures of the system. The number and size of the component hypothetical CSTRlets are calculated from the analytical model and are used to predict temperature profiles at the exit of the system and at intermediate junctions between system components (where thermocouples are present in the actual unit.) The finite element calculations employ a series of CSTRlet volumes to produce a similar suite of temperature profiles, for comparison with the analytical model results. Finally, empirical data from the Factory Acceptance Test system warm-up are used to select and compare the results from each modeling strategy to select the CSTRlet train(s) which best model the behavior of the actual system. This work presents a novel method of system component characterization, of value to the WTP plant and similar vitrification facilities as well as chemical process industries unrelated to waste management. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Investigating the Effect of the Closure in Partially-Averaged Navier–Stokes Equations

For this study, the importance of the turbulence closure to the modeling accuracy of the partially-averaged Navier–Stokes equations (PANS) is investigated in prediction of the flow around a circular cylinder at Reynolds number of 3900. A series of PANS calculations at various degrees of physical resolution is conducted using three Reynolds-averaged Navier–Stokes equations (RANS)-based closures: the standard, shear-stress transport (SST), and turbulent/nonturbulent (TNT) k–ω models. The latter is proposed in this work. The results illustrate the dependence of PANS on the closure. At coarse physical resolutions, a narrower range of scales is resolved so that the influence of the closure on the simulations accuracy increases significantly. Among all closures, PANS–TNT achieves the lowest comparison errors. The reduced sensitivity of this closure to freestream turbulence quantities and the absence of auxiliary functions from its governing equations are certainly contributing to this result. It is demonstrated that the use of partial turbulence quantities in such auxiliary functions calibrated for total turbulent (RANS) quantities affects their behavior. On the other hand, the successive increase of physical resolution reduces the relevance of the closure, causing the convergence of the three models toward the same solution. Finally, this outcome is achieved once the physical resolution and closure guarantee the precise replication of the spatial development of the key coherent structures of the flow.

42 ENGINEERING↗
DOE OSTI2024

How Well Does the DOE Global Storm Resolving Model Simulate Clouds and Precipitation Over the Amazon?

This study assesses a 40-day 3.25-km global simulation of the Simple Cloud-Resolving E3SM Model (SCREAMv0) using high-resolution ground-based observations from the Atmospheric Radiation Measurement (ARM) Green Ocean Amazon (GoAmazon) field campaign. SCREAMv0 reasonably captures the diurnal timing of boundary layer clouds yet underestimates the boundary layer cloud fraction and mid-level congestus. SCREAMv0 well replicates the precipitation diurnal cycle, however it exhibits biases in the precipitation cluster size distribution compared to scanning radar observations. Specifically, SCREAMv0 overproduces clusters smaller than 128 km, and does not form enough large clusters. Such biases suggest an inhibition of convective upscale growth, preventing isolated deep convective clusters from evolving into larger mesoscale systems. This model bias is partially attributed to the misrepresentation of land-atmosphere coupling. This study highlights the potential use of high-resolution ground-based observations to diagnose convective processes in global storm resolving model simulations, identify key model deficiencies, and guide future process-oriented model sensitivity tests and detailed analyses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Recombinant Vaccine Strain ASFV-G-Δ9GL/ΔUK Produced in the IPKM Cell Line Is Genetically Stable and Efficacious in Inducing Protection in Pigs Challenged with the Virulent African Swine Fever Virus Field Isolate Georgia 2010

We have previously reported that the recombinant African Swine Fever (ASF) vaccine candidate ASFV-G-Δ9GL/ΔUK efficiently induces protection in domestic pigs challenged with the virulent strain Georgia 2010 (ASFV-G). As reported, ASFV-G-Δ9GL/ΔUK induces protection, while intramuscularly (IM), administered at doses of 10 4 HAD 50 or higher, prevents ASF clinical disease in animals infected with the homologous ASFV g strain. Like other recombinant vaccine candidates obtained from ASFV field isolates, ASFV-G-Δ9GL/ΔUK stocks need to be produced in primary cultures of swine macrophages, which constitutes an important limitation in the production of large virus stocks at the industrial level. Here, we describe the development of ASFV-G-Δ9GL/ΔUK stocks using IPKM (Immortalized Porcine Kidney Macrophage) cells, which are derived from swine macrophages. We show that ten successive passages of ASFV-G-Δ9GL/ΔUK in IPKM cells induced small changes in the virus genome. The produced virus, ASFV-G-Δ9GL/ΔUKp10, presented a similar level of replication in swine macrophages cultures to that of the original ASFV-G-Δ9GL/ΔUK (ASFV-G-Δ9GL/ΔUKp0). The protective efficacy of ASFV-G-Δ9GL/ΔUKp10 was evaluated in pigs that were IM-inoculated with either 10 4 or 10 6 HAD 50 of ASFV-G-Δ9GL/ΔUKp10. While animals inoculated with 10 4 HAD 50 present a partial protection against the experimental infection with the virulent parental virus ASFV-G, those inoculated with 10 6 HAD 50 were completely protected. Therefore, as was just recently reported for another ASF vaccine candidate, ASFV-G-ΔI177L, IPKM cells are an effective alternative to produce stocks for vaccine strains which only grow in swine macrophages.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Discovering a Transferable Charge Assignment Model Using Machine Learning

Partial atomic charge assignment is of immense practical value to force field parametrization, molecular docking, and cheminformatics. Machine learning has emerged as a powerful tool for modeling chemistry at unprecedented computational speeds given accurate reference data. However, certain tasks, such as charge assignment, do not have a unique solution. We use a machine learning algorithm to discover a new charge assignment model by learning to replicate molecular dipole moments across a large, diverse set of nonequilibrium conformations of molecules containing C, H, N, and O atoms. The new model, called Affordable Charge Assignment (ACA), is computationally inexpensive and predicts dipoles of out-of-sample molecules accurately. Furthermore, dipole-inferred ACA charges are transferable to dipole and even quadrupole moments of much larger molecules than those used for training. We apply ACA to dynamical trajectories of biomolecules and produce their infrared spectra. Additionally, we find that ACA assigns similar charges to Charge Model 5 but with greatly reduced computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The Influenza A Virus Endoribonuclease PA-X Usurps Host mRNA Processing Machinery to Limit Host Gene Expression

Often, many viruses shut off host gene expression to inhibit antiviral responses. Viral proteins and host proteins required for viral replication are typically spared in this process, yet the mechanisms of target selectivity during host shutoff remain poorly understood. Using transcriptome-wide and targeted reporter experiments, we demonstrate that the influenza A virus endoribonuclease PA-X usurps RNA splicing to selectively target host RNAs for destruction. Proximity-labeling proteomics reveals that PA-X interacts with cellular RNA processing proteins, some of which are partially required for host shutoff. Thus, PA-X taps into host nuclear pre-mRNA processing mechanisms to destroy nascent mRNAs shortly after their synthesis. This mechanism sets PA-X apart from other viral host shutoff proteins that target actively translating mRNAs in the cytoplasm. Our study reveals a unique mechanism of host shutoff that helps us understand how influenza viruses suppress host gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP

The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme’s quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α 2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α 2 dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α 2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood–Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community’s capacity, with up to 9.9% of fermentation, 6.4% of the Wood–Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

Candidatus↗
DOE OSTI2020

A Single Amino Acid Substitution in the Matrix Protein (M51R) of Vesicular Stomatitis New Jersey Virus Impairs Replication in Cultured Porcine Macrophages and Results in Significant Attenuation in Pigs

In this study, we explore the virulence of vesicular stomatitis New Jersey virus (VSNJV) in pigs and its potential relationship with the virus’s ability to modulate innate responses. For this purpose, we developed a mutant of the highly virulent strain NJ0612NME6, containing a single amino acid substitution in the matrix protein (M51R). The M51R mutant of NJ0612NME6 was unable to suppress the transcription of genes associated with the innate immune response both in primary fetal porcine kidney cells and porcine primary macrophage cultures. Impaired viral growth was observed only in porcine macrophage cultures, indicating that the M51 residue is required for efficient replication of VSNJV in these cells. Furthermore, when inoculated in pigs by intradermal scarification of the snout, M51R infection was characterized by decreased clinical signs including reduced fever and development of less and smaller secondary vesicular lesions. Pigs infected with M51R had decreased levels of viral shedding and absence of RNAemia compared to the parental virus. The ability of the mutant virus to infect pigs by direct contact remained intact, indicating that the M51R mutation resulted in a partially attenuated phenotype capable of causing primary lesions and transmitting to sentinel pigs. Collectively, our results show a positive correlation between the ability of VSNJV to counteract the innate immune response in swine macrophage cultures and the level of virulence in pigs, a natural host of this virus. More studies are encouraged to evaluate the interaction of VSNJV with macrophages and other components of the immune response in pigs.

59 BASIC BIOLOGICAL SCIENCES↗