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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 OSTI2022

Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro

Abstract Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter “nicking” and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.

Science & Technology - Other Topics↗
DOE OSTI2022

A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation

Biological nitrogen fixation (BNF) is the reduction of N 2 into NH 3 in a group of prokaryotes by an extremely O 2 -sensitive protein complex called nitrogenase. Transfer of the BNF pathway directly into plants, rather than by association with microorganisms, could generate crops that are less dependent on synthetic nitrogen fertilizers and increase agricultural productivity and sustainability. In the laboratory, nitrogenase activity is commonly determined by measuring ethylene produced from the nitrogenase-dependent reduction of acetylene (ARA) using a gas chromatograph. The ARA is not well suited for analysis of large sample sets nor easily adapted to automated robotic determination of nitrogenase activities. Here, we show that a reduced sulfonated viologen derivative (S 2 V red ) assay can replace the ARA for simultaneous analysis of isolated nitrogenase proteins using a microplate reader. We used the S 2 V red to screen a library of NifH nitrogenase components targeted to mitochondria in yeast. Two NifH proteins presented properties of great interest for engineering of nitrogen fixation in plants, namely NifM independency, to reduce the number of genes to be transferred to the eukaryotic host; and O 2 resistance, to expand the half-life of NifH iron-sulfur cluster in a eukaryotic cell. This study established that NifH from Dehalococcoides ethenogenes did not require NifM for solubility, [Fe-S] cluster occupancy or functionality, and that NifH from Geobacter sulfurreducens was more resistant to O 2 exposure than the other NifH proteins tested. It demonstrates that nitrogenase components with specific biochemical properties such as a wider range of O 2 tolerance exist in Nature, and that their identification should be an area of focus for the engineering of nitrogen-fixing crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mechanically tunable elastomer and cellulose nanocrystal composites as scaffolds for in vitro cell studies

Considering the range of properties that various materials offer for tissue engineering it has come clear that no one size fits all, as no one material can be fully effective for all types of cell and ensuing tissues. Scaffolds need to address the delicate balance between cell-scaffold interactions and the particular requirements of different cell types. To address the specific needs for the controlled growth of tissues it is imperative to match scaffold stiffness and elasticity to cells and tissues of interest to promote regeneration success. We here report an efficient method for creating scaffolds of tunable elasticity by generating a range of composites based on ε-caprolactone-D,L-lactide-based elastomer with cellulose nanocrystals (CNC). Two specific composites with different Young's modulus (E) values (~5 MPa and ~15 MPa) were selected and fully evaluated by tensile tests, Fourier Transform-Infrared (FT-IR), Scanning Electron Microscopy (SEM), contact angle measurements, and X-ray scattering. As a proof of concept this work studies how matching the scaffold's mechanical properties to neuroblastomas and fibroblasts cells affects cell behavior. Specifically, the composite with lower E, by design with less CNC content, is more suitable for neuroblastomas, whereas the one with higher E via higher CNC content is more suited for human dermal fibroblasts. The approach of matching cells with appropriate mechanical environments can provide important insights into fundamental cell behaviors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Photochemistry and in vitro anticancer activity of Pt(IV)Re(I) conjugates

The photophysical and photochemical properties of two Pt(IV)Re(I) conjugates were studied via both experimental and computational methods. Additionally, both conjugates exhibit modest photocytotoxicity against ovarian cancer cells. X-ray fluorescence microscopy showed that Pt and Re colocalize in cells whether they had been irradiated or not. This work demonstrates the potential of photoactivated multilimetallic agents for combating cancer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca 2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Integrating Data From In Vitro New Approach Methodologies for Developmental Neurotoxicity

Abstract In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array neuronal network formation assay; and high-content imaging to evaluate proliferation, apoptosis, neurite outgrowth, and synaptogenesis. This work addresses 3 hypotheses: (1) a broad screening battery provides a sensitive marker of DNT bioactivity; (2) selective bioactivity (occurring at noncytotoxic concentrations) may indicate functional processes disrupted; and, (3) a subset of endpoints may optimally classify chemicals with in vivo evidence for DNT. The dataset was comprised of 92 chemicals screened in all 57 assay endpoints sourced from publicly available data, including a set of DNT NAM evaluation chemicals with putative positives (53) and negatives (13). The DNT NAM battery provides a sensitive marker of DNT bioactivity, particularly in cytotoxicity and network connectivity parameters. Hierarchical clustering suggested potency (including cytotoxicity) was important for classifying positive chemicals with high sensitivity (93%) but failed to distinguish patterns of disrupted functional processes. In contrast, clustering of selective values revealed informative patterns of differential activity but demonstrated lower sensitivity (74%). The false negatives were associated with several limitations, such as the maximal concentration tested or gaps in the biology captured by the current battery. This work demonstrates that this multi-dimensional assay suite provides a sensitive biomarker for DNT bioactivity, with selective activity providing possible insight into specific functional processes affected by chemical exposure and a basis for further research.

Carstens, Kelly E.↗
DOE OSTI2023

Hooks versus Pedicle Screws at the Upper Instrumented Level: An In Vitro Biomechanical Comparison

Study Design. Controlled laboratory study Objective. To compare motions at the upper instrumented vertebra (UIV) and supra-adjacent level (UIV+1) between two fixation techniques in thoracic posterior spinal fusion (PSF) constructs. We hypothesized there would be greater motion at UIV+1 after cyclic loading across all constructs and bilateral pedicle screws (BPS) with posterior ligamentous compromise would demonstrate the greatest UIV+1 range of motion (ROM). Summary of Background Data. Proximal junctional kyphosis (PJK) is a well-recognized complication following long thoraco-lumbar PSF, however its mechanism is poorly understood. Methods. Twenty-seven thoracic functional spine units (FSU) were randomly divided into three UIV fixation groups (n=9): (1) BPS, (2) bilateral transverse process hooks (TPH), and (3) BPS with compromise of the posterior elements between UIV and UIV+1 (BPS-C). Specimens were tested on a servohydraulic materials testing system in native state, following instrumentation, and after cyclic loading. FSUs were loaded in flexion-extension (FE), lateral bending (LB), and axial rotation (AR). Results. After cyclic testing, the TPH group had a mean 29.4% increase in FE ROM at UIV+1 versus 76.6% in the BPS group ( P <0.05). The BPS-C group showed an increased FE of 49.9% and 62.19% with sectioning of the facet joints and interspinous ligament respectively prior to cyclic testing. Conclusion. Bilateral pedicle screws at the UIV led to greater motion at UIV+1 compared to bilateral TPH after cyclic loading. This is likely due to the increased rigidity of BPS compared to TPH leading to a “softer” transition between the TPH construct and native anatomy at the supra-adjacent level. Facet capsule compromise led to a 49.9% increase in UIV+1 motion, underscoring the importance of preserving the posterior ligamentous complex. Clinical studies that account for fusion rates are warranted to determine if constructs with a “soft transition” result in less PJK in vivo.

Neurosciences & Neurology↗
DOE OSTI2024

In vitro evidence that the vasorelaxant effects of 2‐nitro‐1‐phenyl‐1‐propanol on rat coronary arteries involve cyclic nucleotide pathways

Abstract The synthetic nitro‐alcohol 2‐nitro‐1‐phenyl‐1‐propanol (NPP) has endothelium‐independent relaxing properties in isolated preparations of rat aorta and mesenteric artery. In this study, we investigated whether the vasodilator effects occur in coronary vessels and explored whether hyperpolarization is involved in the underlying mechanism of NPP‐induced smooth muscle relaxation. The relaxing responses were studied in isolated preparations of the left anterior descending coronary (ADC) and the septal coronary (SC) arteries, which had been previously maintained under sustained contraction induced by the thromboxane A 2 analogue U‐46619. Administered cumulatively, NPP elicited concentration‐dependent vasorelaxation with similar potency in both vessels. The relaxant effect remained unaffected by the nitric oxide synthase inhibitor L‐NAME, the protein kinase C inhibitor bisindolylmaleimide IV and the Rho‐associated protein kinase inhibitor Y‐27632. However, it was significantly diminished by the adenylyl cyclase inhibitor MDL‐12,330A, the guanylyl cyclase inhibitor ODQ, as well as the K + channel inhibitors tetraethylammonium and CsCl. In ADC preparations impaled with intracellular micropipettes, NPP hyperpolarized the vascular preparation. When the isolated preparation was precontracted by 5‐hydroxytryptamine or 80 mM KCl, NPP‐induced relaxation with lower pharmacological potency compared to the vessels contracted by U‐46619. In conclusion, NPP exhibits vasorelaxant effects on rat coronary arteries, likely involving pathways that include cyclic nucleotide production and membrane hyperpolarization.

Vasconcelos‐Silva, Alfredo Augusto↗
DOE OSTI2020

Anti‐adhesive effects of sialic acid and Lactobacillus plantarum on Staphylococcus aureus in vitro

Abstract Staphylococcus aureus (S. aureus) is a common food‐borne pathogen that causes severe diseases after adhesion to epithelial cells. Lactobacillus inhibits pathogenic bacterial adhesion and infection. In addition, sialic acid (SA) is widely known for its beneficial biological functions. A new way of reducing the occurrence of diseases and curbing the overuse of antibiotics is ingesting prebiotics and probiotics that regulate the intestinal flora. In this study, we first evaluated the anti‐adhesive effects of several strains of Lactobacillus on S. aureus . The study revealed that the S. aureus adhesion was inhibited by all the strains of Lactobacillus . Besides, the rate of inhibition by L. plantarum Z‐4 was significantly higher than other Lactobacillus species . We then investigated the effects of different SA concentrations (40, 100, 150, 200, and 260 μg/ml) on the growth and adhesion characteristics of L. plantarum and S. aureus . The results showed that SA influences bacterial adhesion by regulating the bacteria's growth characteristics. Finally, the effects of SA combined with Lactobacillus on the adhesion of S. aureus were assessed by competition, exclusion and displacement methods. SA with a concentration of 260 μg/mL combined with L. plantarum had the highest inhibition effect on the competition assays. In addition, the expression of S. aureus adhesion‐related genes was reduced. This provides a new perspective on the application of SA and/or L. plantarum and its potential to resist adhesion of S. aureus .

Lu, Yingying↗
DOE OSTI2020

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice

Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Using DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium aromaticivorans DSM12444 transcription factors

Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.

DAP-seq↗