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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 361 records · Page 20

An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ

The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.

59 BASIC BIOLOGICAL SCIENCES↗

The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.

60 APPLIED LIFE SCIENCES↗

The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA

CDCA7, encoding a protein with a carboxyl-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.

Science & Technology - Other Topics↗

Structure of coxsackievirus cloverleaf RNA and 3C pro dimer establishes the RNA-binding mechanism of enterovirus protease 3C pro

In positive-strand RNA viruses, the genome serves as a template for both protein translation and negative-strand RNA synthesis. Enteroviruses use the cloverleaf RNA structure at the 5′ end of the genome to balance these two processes. Cloverleaf acts as a promoter for RNA synthesis and forms a complex with viral 3CD protein, the precursor to 3C pro protease, and 3D pol polymerase. The interaction between cloverleaf and 3CD is mediated by the 3C pro domain, yet how 3C pro promotes specific RNA-binding is not clear. We report the structure of coxsackievirus cloverleaf RNA-3C pro complex, wherein two 3C pro molecules interact with cloverleaf stem-loop D. 3C pro dimer mainly recognizes the shape of the dsRNA helix through symmetric interactions, suggesting that 3C pro is a previously undiscovered type of RNA binding protein. We show that 3CD protein also dimerizes on cloverleaf RNA and binds the RNA with higher affinity than 3C pro . The structure provides insight into the RNA-binding mechanism of 3C pro or 3CD with other cis-acting replication elements.

Science & Technology - Other Topics↗

Topology-imprinting in nonlinear metasurfaces

Flat optical components, or metasurfaces, have transformed optical imaging, data storage, information processing, and biomedical applications by providing unprecedented control over light-matter interactions. These nano-engineered structures enable compact, multidimensional manipulation of light’s amplitude, phase, polarization, and wavefront, producing scalar and vector beams with unique properties such as orbital angular momentum and knotted topologies. This flexibility has potential applications in optical communication and imaging, particularly in complex environments such as atmospheric turbulence and undersea scattering. However, designing metasurfaces for shorter wavelengths, such as visible and ultraviolet light, remains challenging due to fabrication limitations and material absorption. Here, we introduce an innovative concept called topology imprinting using judiciously designed all-dielectric nonlinear optical metasurfaces to replicate desired waveforms at fundamental and harmonic frequencies, opening promising avenues for advanced photonic applications.

42 ENGINEERING↗

Robust measurement of microbial reduction of graphene oxide nanoparticles using image analysis

ABSTRACT Shewanella oneidensis ( S. oneidensis ) has the capacity to reduce electron acceptors within a medium and is thus used frequently in microbial fuel generation, pollutant breakdown, and nanoparticle fabrication. Microbial fuel setups, however, often require costly or labor-intensive components, thus making optimization of their performance onerous. For rapid optimization of setup conditions, a model reduction assay can be employed to allow simultaneous, large-scale experiments at lower cost and effort. Since S. oneidensis uses different extracellular electron transfer pathways depending on the electron acceptor, it is essential to use a reduction assay that mirrors the pathways employed in the microbial fuel system. For microbial fuel setups that use nanoparticles to stimulate electron transfer, reduction of graphene oxide provides a more accurate model than other commonly used assays as it is a bulk material that forms flocculates in solutions with a large ionic component. However, graphene oxide flocculates can interfere with traditional absorbance-based measurement techniques. This study introduces a novel image analysis method for quantifying graphene oxide reduction, showing improved performance and statistical accuracy over traditional methods. A comparative analysis shows that the image analysis method produces smaller errors between replicates and reveals more statistically significant differences between samples than traditional plate reader measurements under conditions causing graphene oxide flocculation. Image analysis can also detect reduction activity at earlier time points due to its use of larger solution volumes, enhancing color detection. These improvements in accuracy make image analysis a promising method for optimizing microbial fuel cells that use nanoparticles or bulk substrates. IMPORTANCE Shewanella oneidensis ( S. oneidensis ) is widely used in reduction processes such as microbial fuel generation due to its capacity to reduce electron acceptors. Often, these setups are labor-intensive to operate and require days to produce results, so use of a model assay would reduce the time and expenses needed for optimization. Our research developed a novel digital analysis method for analysis of graphene oxide flocculates that may be utilized as a model assay for reduction platforms featuring nanoparticles. Use of this model reduction assay will enable rapid optimization and drive improvements in the microbial fuel generation sector.

Bennett, Danielle T. (ORCID:0009000188748827)↗

The Thermococcales as a model system: historical perspectives and emerging tools

Thermococcales are among the most widely studied hyperthermophilic Archaea and have become key models for understanding life at extreme temperatures. Early work in the 1980s culminated in the isolation of novel Thermococcales species from hydrothermal vents that grew rapidly, tolerated extreme heat, and metabolized diverse substrates, making them uniquely amenable for laboratory studies. Their thermostable enzymes and emerging genetic tools facilitated detailed investigations of core processes such as DNA replication, repair, and transcription under conditions that challenge most life forms. These practical advantages, together with the accumulation of tools and protocols, cemented the role of Thermococcales as a model system. Here, we recount how chance discoveries, environmental adaptations, and experimental practicality intersected to establish Thermococcales as a central model for studying archaeal biology and extremophile physiology.

59 BASIC BIOLOGICAL SCIENCES↗

Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors

Human norovirus (HuNoV) is a leading cause of gastroenteritis worldwide and is associated with significant morbidity, mortality, and economic impact. There are currently no licensed antiviral drugs for the treatment of HuNoV-associated gastroenteritis. The HuNoV protease plays a critical role in the initiation of virus replication by cleaving the polyprotein. Thus, it is an ideal target for developing antiviral small-molecule inhibitors. While rupintrivir, a potent small-molecule inhibitor of several picornavirus proteases, effectively inhibits GI.1 protease, it is an order of magnitude less effective against GII protease. Other GI.1 protease inhibitors also tend to be less effective against GII proteases. To understand the structural basis for the potency difference, we determined the crystal structures of proteases of GI.1, pandemic GII.4 (Houston and Sydney), and GII.3 in complex with rupintrivir. These structures show that the open substrate pocket in GI protease binds rupintrivir without requiring significant conformational changes, whereas, in GII proteases, the closed pocket flexibly extends, reorienting arginine-112 in the BII-CII loop to accommodate rupintrivir. Structures of R112A protease mutants with rupintrivir, coupled with enzymatic and inhibition studies, suggest R112 is involved in displacing both substrate and ligands from the active site, implying a role in the release of cleaved products during polyprotein processing. Thus, the primary determinant for differential inhibitor potency between the GI and GII proteases is the increased flexibility in the BII-CII loop of the GII proteases caused by the H-G mutation in this loop. Therefore, the inherent flexibility of the BII-CII loop in GII proteases is a critical factor to consider when developing broad-spectrum inhibitors for HuNoV proteases.

60 APPLIED LIFE SCIENCES↗

Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East respiratory syndrome coronavirus disease severity

Coronaviruses (CoV) emerge suddenly from animal reservoirs to cause novel diseases in new hosts. Discovered in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in camels in the Middle East and is continually causing local outbreaks and epidemics. While all three newly emerging human CoVs from the past 20 years (SARS-CoV, SARS-CoV-2, and MERS-CoV) cause respiratory disease, each CoV has unique host interactions that drive differential pathogeneses. To better understand the virus and host interactions driving lethal MERS-CoV infection, we performed a longitudinal multi-omics analysis of sublethal and lethal MERS-CoV infection in mice. Significant differences were observed in body weight loss, virus titers, and acute lung injury among lethal and sub-lethal virus doses. Virus-induced apoptosis of type I and II alveolar epithelial cells suggests that loss or dysregulation of these key cell populations was a major driver of severe disease. Omics analysis suggested differential pathogenesis was multi-factorial with clear differences among innate and adaptive immune pathways as well as those that regulate lung epithelial homeostasis. Infection of mice lacking functional T and B cells showed that adaptive immunity was important in controlling viral replication but also increased pathogenesis. In summary, we provide a high-resolution host response atlas for MERS-CoV infection and disease severity. Multi-omics studies of viral pathogenesis offer a unique opportunity to not only better understand the molecular mechanisms of disease but also to identify genes and pathways that can be exploited for therapeutic intervention all of which is important for our future pandemic preparedness.

MERS-CoV↗

Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient

In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO43-). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO43- from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO₄³⁻ and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO₄³-. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.

arbuscular mycorrhizal fungi↗

Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS)

ABSTRACT Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma–optical emission spectroscopy (ICP-OES) and inductively coupled plasma–mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique—one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment. IMPORTANCE Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.

59 BASIC BIOLOGICAL SCIENCES↗

Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Chen, Jianhai (ORCID:0000000300932003)↗

New results in the CTEQ-TEA global analysis of parton distributions in the nucleon

This report summarizes the latest developments in the CTEQ-TEA global analysis of parton distribution functions (PDFs) in the nucleon. The focus is on recent NNLO fits to high-precision LHC data at 8 and 13 TeV, including Drell–Yan, jet, and top-quark pair production, pursued on the way toward the release of the new generation of CTEQ-TEA general-purpose PDFs. The report also discusses advancements in statistical and numerical methods for PDF determination and uncertainty quantification, highlighting the importance of robust and replicable uncertainties for high-stakes observables. Additionally, it covers phenomenological studies related to PDF determination, such as the interplay of experimental constraints, exploration of correlations between high-x nucleon sea and low-energy parity-violating measurements, fitted charm in the nucleon, the photon PDF in the neutron, and simultaneous SMEFT-PDF analyses.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

GreenThrift: Optimizing Carbon and Cost for Flexible Residential Loads

Reducing buildings’ carbon emissions is an important sustainability challenge. While scheduling flexible building loads has been previously used for a variety of grid and energy optimizations, carbon footprint reduction using such flexible loads poses new challenges since such methods need to balance both energy and carbon costs while also reducing user inconvenience from delaying such loads. This paper highlights the potential conflict between electricity prices and carbon emissions and the resulting trade-offs in carbon-aware and cost-aware load scheduling. To address this trade-off, we propose GreenThrift, a home automation system that leverages the scheduling capabilities of smart appliances and knowledge of future carbon intensity and cost to reduce both the carbon emissions and costs of flexible energy loads. At the heart of GreenThrift is an optimization technique that automatically computes schedules based on user configurations and preferences. We evaluate the effectiveness of GreenThrift using real-world carbon intensity data, electricity prices, and load traces from multiple locations and across different scenarios and objectives. Our results show that GreenThrift can replicate the offline optimal and retains 97% of the savings when optimizing the carbon emissions. Moreover, we show how GreenThrift can balance the conflict between carbon and cost and retain 95.3% and 85.5% of the potential carbon and cost savings, respectively.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A Digital Twin of Scalable Quantum Clouds

Quantum computing has emerged as a transformative technology capable of solving complex problems beyond the limit of classical systems. The rapid development of quantum processors has led to the proliferation of cloud-based quantum computing services offered by platforms such as IBM, Google, and Amazon. These platforms introduce unique challenges in resource allocation, job scheduling, and multi-device orchestration as quantum workloads become increasingly complex. In this work, we present a digital twin of quantum cloud infrastructures: a framework designed to model and simulate the behavior of real quantum cloud systems. Developed in Python using the SimPy discrete-event simulation library, the framework replicates key aspects of quantum cloud environments, including detailed quantum device modeling, job lifecycle management, and job fidelity. It incorporates noise-aware fidelity estimation, making it the first of its kind to simulate superconducting gate-based quantum cloud systems at an administrative level with job fidelity. We present use cases as proof of concept, demonstrating that our quantum cloud simulation framework can act as a digital twin of a quantum cloud and support the modeling and implementation of practical systems.

Luo, Waylon [Kent State University]↗

Lattice Effective Field Theory Simulations of Nuclei

Lattice effective field theory applies the principles of effective field theory in a lattice framework where space and time are discretized. Nucleons are placed on the lattice sites, and the interactions are tuned to replicate the observed features of the nuclear force. Monte Carlo simulations are then employed to predict the properties of nuclear few- and many-body systems. Here, we review the basic methods and several theoretical and algorithmic advances that have been used to further our understanding of atomic nuclei.

nuclear lattice effective field theory↗

Factors Controlling Electrochemistry-Induced Deposition of a Zeolitic Imidazolate Framework-8 Film on Underlying Substrates

This paper discusses factors controlling electrochemistry-induced deposition of a zeolitic imidazolate framework-8 (ZIF-8) film on a planar substrate that is placed under an electrode. This method, which was recently demonstrated by us [T. Ito, et al. Cryst. Growth Des., 23, 6369 (2023)], provides a simple means to form a ZIF-8 film having lateral dimensions replicating those of a working electrode on an underlying substrate. We reported the effects of applied cathodic potential, electrode–substrate distance, and deposition time on the film formation, and proposed a mechanism involving cathodic base generation at a working electrode that promoted ligand deprotonation to form intermediate species, followed by their diffusion toward an underlying substrate. Here, we discuss details on the deposition mechanism by investigating the influences of other factors on the film deposition. We have investigated the effects of precursor concentration on film formation, and clarified that O 2 is a probase, rather than H 2 O. We have also shown the influences of substrate surface properties controlled by self-assembled monolayers on film thickness and morphology. Most notably, we successfully demonstrated the formation of microscale ZIF-8 films using an ultramicroelectrode, revealing the applicability of the electrochemistry-induced method for micropatterned film deposition on an underlying substrate.

36 MATERIALS SCIENCE↗

Building High-Energy Silicon-Containing Batteries Using Off-The-Shelf Materials

The technology of silicon anodes appears to be reaching maturity, with high-energy Si cells already in pilot-scale production. However, the performance of these systems can be difficult to replicate in academic settings, making it challenging to translate research findings into solutions that can be implemented by the battery industry. Part of this difficulty arises from the lack of access to engineered Si particles and anodes, as electrode formulations and the materials themselves have become valuable intellectual property for emerging companies. Here, we summarize the efforts by Argonne’s Cell Analysis, Modeling, and Prototyping (CAMP) Facility in developing Si-based prototypes made entirely from commercially available materials. We describe the many challenges we encountered when testing high-loading electrodes (>5 mAh cm −2 ) and discuss strategies to mitigate them. With the right electrode and electrolyte design, we show that our pouch cells containing ≥ 70 wt% SiO x can achieve 600–1,000 cycles at C/3 and meet projected energy targets of 700 Wh L −1 and 350 Wh kg −1 . These results provide a practical reference for research teams seeking to advance silicon-anode development using accessible materials.

25 ENERGY STORAGE↗