Search NASA⌕ Search

SEARCH · Search NASA

Results for “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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication

The recent rise in zoonotic coronavirus outbreaks underscores the urgency to understand virus-host interactions and develop potent antiviral therapeutics. Systems biology approaches, particularly proteomics have been invaluable in providing a global overview of such interactions. However, these conventional approaches rely on measuring protein abundance changes which don’t reflect functional shifts. In this study, we employed a high-throughput structural proteomics approach called limited proteolysis-based mass spectrometry (LiP-MS) to capture conformational changes, which we demonstrate are better proxies for functional alterations. We applied this tool to both immortalized and primary human lung cells following human coronavirus 229E (HCoV-229E) infection. We identified significant infection-induced structural changes within RNA processing complexes such as the spliceosome-C and NOP56-associated complex. These observations emphasize that HCoV-229E infection propagates a multi-pronged effort to obstruct the house keeping RNA processing functions in the host. Finally, we show that HCoV-229E replication can be attenuated by the targeted disruption of these complexes, indicating that the identified cellular factories are viable targets to prevent coronavirus infection.

coronavirus↗
DOE OSTI2025

S -Adenosylhomocysteine Analogs Selectively Suppress Pan-Coronavirus Replication by Inhibition of nsp14 Methyltransferase

To address the ongoing threat of SARS-CoV-2 and potential emergence of novel coronaviruses, we employed a comprehensive strategy to identify and synthesize inhibitors of coronavirus methyltransferases with chemical analogs of S-adenosylhomocysteine (SAH). Two analogs, designated 4h and 4p, inhibit both mouse hepatitis virus and SARS-CoV-2 replication. Compound 4p was the most potent with half-maximal inhibition of biochemical activity at 0.2 μM and antiviral activity at ∼20 μM. This compound also has low cytotoxicity and preferentially inhibits nsp14 over nsp16 and human methyltransferases. Furthermore, molecular docking based on a newly determined crystal structure of the apo nsp16−nsp10 complex predicts that 4p occupies both the Sadenosylmethione and Gppp binding pockets of nsp14 and nsp16. Selectivity of 4p for nsp14 is likely due to the enhanced structural stability of the nsp14 binding pocket relative to nsp16. These findings highlight SAH analogs as scaffolds for pan-coronavirus therapeutics and underscore the value of structure-guided design in antiviral drug discovery.

Coronavirus↗
DOE OSTI2025

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter

Abstract The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution inSaccharomyces cerevisiaethat diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporterJEN1 (JEN1t)into a de novo mevalonate importer. We demonstrate the functionality of the evolvedJEN1t(JEN1t Y180C/G ) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Enhancing quantum annealing accuracy through replication-based error mitigation *

Abstract Quantum annealers like those manufactured by D-Wave Systems are designed to find high quality solutions to optimization problems that are typically hard for classical computers. They utilize quantum effects like tunneling to evolve toward low-energy states representing solutions to optimization problems. However, their analog nature and limited control functionalities present challenges to correcting or mitigating hardware errors. As quantum computing advances towards applications, effective error suppression is an important research goal. We propose a new approach called replication based mitigation (RBM) based on parallel quantum annealing (QA). In RBM, physical qubits representing the same logical qubit are dispersed across different copies of the problem embedded in the hardware. This mitigates hardware biases, is compatible with limited qubit connectivity in current annealers, and is well-suited for currently available noisy intermediate-scale quantum annealers. Our experimental analysis shows that RBM provides solution quality on par with previous methods while being more flexible and compatible with a wider range of hardware connectivity patterns. In comparisons against standard QA without error mitigation on larger problem instances that could not be handled by previous methods, RBM consistently gets better energies and ground state probabilities across parameterized problem sets.

Djidjev, Hristo N. (ORCID:0000000192868824)↗
DOE OSTI2024

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Replicative Assessment of Spectroscopic Equipment v3.1

The Replicative Assessment of Spectrometric Equipment (RASE) is a software for evaluating the performance of radiation detectors and isotope identification algorithms. It uses a semi-empirical approach to rapidly generate synthetic spectra and inject into detector's software to obtain nuclide identification response. RASE facilitates studies of spectroscopic device performance and a quantitative assessment of its capabilities to correctly distinguish and identify isotopes of interest in realistic scenarios

Sangiorgio, Samuele [Lawrence Livermore National L↗
DOE OSTI2024

EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations

Introduction Studying plant-microbe interactions is one of the key elements in understanding the path to sustainable agricultural practices. These interactions play a crucial role in ensuring survival of healthy plants, soil and microbial communities. Many platforms have been developed over the years to isolate these highly complex interactions however, these are designed for small model plants. This creates a need for complementary devices for larger plants, such as sorghum. Methods This work introduces a novel platform, EcoFAB 3.0, which is designed to enable studying bioenergy plants such as sorghum for up to 4 weeks in a controlled sterile environment. Several other advantages of this platform such as dark root chambers and user-friendly assembly are also discussed in this work. Results and discussion EcoFAB 3.0 was found to replicate previous greenhouse and field observations when comparing an engineered sorghum line overproducing 4-hydroxybenzoic acid (4-HBA) and wildtype (variety BTx430). Consistent with greenhouse and field observations, it was found that the engineered line of sorghum grown in EcoFAB 3.0 had a higher 4-HBA content and a lower dry biomass.

Gupta, Kshitiz↗
DOE OSTI2024

Replication Package for "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifier

This replication package is a case study on automated deductive verification for Rust for practical programs. It is a companion artifact to a corresponding usability study on verification titled "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifiers". It seeks to answer the question "Can Rust developers today use Rust verifiers to verify their code?". To answer this question, the study contrasts the verification experience of two mature Rust verifiers, Creusot and Prusti, by using the tools to develop a verified implementation of union-find in Rust. The union-find implementation is based on real-world code as used in the popular egg E-graph library. The artifact consists of two different verified libraries, one using Creusot and one using Prusti. The libraries have similar Rust interfaces and high-level proofs but differ in their details: Creusot and Prusti have different annotation languages and support different proof styles. Each implementation can be verified with its respective tool and compiles as a traditional Rust development.

Sarracino, John↗
NASA NTRS1977

A passive chevron replicator

Instrument design provides replicate function between device storage area and guardrail detector in order that nondestructive read-out of memory can be achieved. Use of guardrail detectors in magnetic domain (bubble) circuits is proposed method of increasing detector signal output by increasing detector size without dedicating an excessive amount of device chip area to detector portion.

Oeffinger, T. R.↗