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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Site-selective tyrosine bioconjugation via photoredox catalysis for native-to-bioorthogonal protein transformation

The growing prevalence of synthetically modified proteins in pharmaceuticals and materials has exposed the need for efficient strategies to enable chemical modifications with high site-selectivity. While genetic engineering can incorporate non-natural amino acids into recombinant proteins, regioselective chemical modification of wild-type proteins remains a challenge. In this work, we use photoredox catalysis to develop a site-selective tyrosine bioconjugation pathway that incorporates bioorthogonal formyl groups, which subsequently allows for the synthesis of structurally defined fluorescent conjugates from native proteins. A water-soluble photocatalyst, lumiflavin, has been shown to induce oxidative coupling between a previously unreported phenoxazine dialdehyde tag and a single tyrosine site, even in the presence of multiple tyrosyl side chains, through the formation of a covalent C–N bond. A variety of native proteins, including those with multiple tyrosines, can successfully undergo both tyrosine-specific and single-site-selective labelling. This technology directly introduces aldehyde moieties onto native proteins, enabling rapid product diversification using an array of well-established bioorthogonal functionalization protocols including the alkyne–azide click reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Abstract Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N 6 -methyladenosine (m 6 A) modifications near the 3′ end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m 6 As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m 6 A ensembles, and maintaining multiple of these m 6 As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2005

Modifying Silicates for Better Dispersion in Nanocomposites

An improved chemical modification has been developed to enhance the dispersion of layered silicate particles in the formulation of a polymer/silicate nanocomposite material. The modification involves, among other things, the co-exchange of an alkyl ammonium ion and a monoprotonated diamine with interlayer cations of the silicate. The net overall effects of the improved chemical modification are to improve processability of the nanocomposite and maximize the benefits of dispersing the silicate particles into the polymer. Some background discussion is necessary to give meaning to a description of this development. Polymer/silicate nanocomposites are also denoted polymer/clay composites because the silicate particles in them are typically derived from clay particles. Particles of clay comprise layers of silicate platelets separated by gaps called "galleries." The platelet thickness is 1 nm. The length varies from 30 nm to 1 m, depending on the silicate. In order to fully realize the benefits of polymer/silicate nanocomposites, it is necessary to ensure that the platelets become dispersed in the polymer matrices. Proper dispersion can impart physical and chemical properties that make nanocomposites attractive for a variety of applications. In order to achieve nanometer-level dispersion of a layered silicate into a polymer matrix, it is typically necessary to modify the interlayer silicate surfaces by attaching organic functional groups. This modification can be achieved easily by ion exchange between the interlayer metal cations found naturally in the silicate and protonated organic cations - typically protonated amines. Long-chain alkyl ammonium ions are commonly chosen as the ion-exchange materials because they effectively lower the surface energies of the silicates and ease the incorporation of organic monomers or polymers into the silicate galleries. This completes the background discussion. In the present improved modification of the interlayer silicate surfaces, the co-ion exchange strengthens the polymer/silicate interface and ensures irreversible separation of the silicate layers. One way in which it does this is to essentially tether one amine of each diamine molecule to a silicate surface, leaving the second amine free for reaction with monomers during the synthesis of a polymer. In addition, the incorporation of alkyl ammonium ions into the galleries at low concentration helps to keep low the melt viscosity of the oligomer formed during synthesis of the polymer and associated processing - a consideration that is particularly important in the case of a highly cross-linked, thermosetting polymer. Because of the chemical bonding between the surface-modifying amines and the monomers, even when the alkyl ammonium ions become degraded at high processing temperature, the silicate layers do not aggregate and, hence, nanometer-level dispersion is maintained.

Campbell, Sandi↗
NASA NTRS2000

Evidence for a Trapped Radical (OH) on Ariel, Oberon, and Titania from Hubble Space Telescope Ultraviolet Spectra

The moons Ariel, Titania, and Oberon have orbits lying within the magnetosphere of Uranus, exposing them to particle irradiation from trapped Ions. This Is similar to the situation experienced by the jovian moons Europa, Ganymede, and Callisto, as well as the saturnian satellites Enceladus, Tethys, Dione, and Rhea. Identification of SO2 on Europa, Ganymede and Callisto, and O3 on Ganymede, Rhea, and Dione has supported suggestions that chemical modifications occur on icy bodies due to ion bombardment associated with the particles entrained within the magnetospheric fields of Jupiter and Saturn. Similar to the Jovian and saturnian satellites mentioned above, water ice is a major component on the larger uranian satellites", thus one might anticipate chemical modification to he an important process in the uranian system. Laboratory studies or the interaction of ultraviolet (uv) and charged-particle radiation with water ice show that in addition to molecular species, a variety of radicals are also produced. We report here evidence for an uv absorption feature in the spectra of Ariel, Titania, and Oberon that we identify as due, in part, to OH; providing the first evidence of a radical produced and trapped on an icy moon within our solar system.

Roush, Ted L.↗
DOE OSTI2021

Structural modification of fentanyls for their retrospective identification by gas chromatographic analysis using chloroformate chemistry

Abstract The one-step breakdown and derivatization of a panel of nine fentanyls to yield uniquely tagged products that can be detected by Electron Ionization Gas Chromatography-Mass Spectrometry (EI-GC-MS) is presented. The method involves the treatment of the synthetic opioids with 2,2,2-trichloroethoxycarbonyl chloride (TrocCl) at 60 °C for 3 h in dichloromethane and furnishes two products from one fentanyl molecule that can be used to retrospectively identify the original opioid. Parameters that were studied and fully optimized for the method included temperature, solvent, nature of scavenging base and reaction time. One of the two resulting products from the reaction bears the trichloroethoxycarbonyl (Troc) tag attached to the norfentanyl portion of the original opioid and greatly aids in the opioid detection and identification process. The methodology has been applied to the chemical modification of a panel of nine fentanyls and in all cases the molecular ion peak for the Troc-norfentanyl product bearing the distinctive trichloroethyl isotopic signature can be clearly observed. The method’s LLOD was determined to be 10 ng/mL while its LLOQ was found to be 20 ng/mL. This methodology represents the first application of chloroformates in the chemical modification of this class of synthetic opioids that are notoriously inert to common derivatization strategies available for GC–MS analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Use of a Lignin-Based Admixture for Tailoring the Rheological Properties of Mortars for 3D Printing: Preprint

Efforts toward decarbonizing construction materials and industrial processes related to cement and concrete can be aided via multifaceted approaches that target alternative admixtures as well as precision control of fabrication. Chemical admixtures for water reduction have played a crucial role in the development of advanced concrete mixtures. Newer biomass processing techniques developed for aviation fuel production from corn stover biomass produce a more reactive lignin byproduct that is suitable for chemical modifications to mimic the properties of polycarboxylate ether admixtures with a smaller carbon footprint. The present study examines the use of lignin-based water-reducing admixture in cement pastes and mortar mixtures for 3D printing. The experimental program explores the use of different dosages of lignin-based admixture to produce 3D-printed samples with appropriate extrudability and buildability. The rheological characterization was performed to determine the flow curve of various mixtures. Finally, the heat of hydration of cement pastes was monitored via isothermal calorimetry to assess the impact of lignin-based admixtures on the hydration process of cement. The results of this study indicate that the use of biomass by-products, such as lignin-based admixtures have great potential to effectively control the fresh-state properties of cement-based materials.

bio-based admixtures↗
DOE OSTI2026

Oxidative Deboronation of Boronic Acids by Hydrogen Peroxide in Planta Generates Borate for Cross-Linking of Rhamnogalacturonan II

Vascular plants require boron to cross-link the rhamnogalacturonan-II (RG-II) domain of pectin to form functional cell walls. Boronic acids, which form reversible esters with cis-diols like borate, have been proposed to influence RG-II cross-linking, though the mechanism remains unclear. We used suspension-cultured rose cells adapted to grow without boron to investigate the effect of boronic acids on RG-II dimerization. When grown with phenylboronic acid (PBA) as the sole boron source, nearly all RG-II was crosslinked, whereas methylboronic acid (MBA) only partially restored cross-linking. In contrast, in vitro assays showed that homogeneous RG-II monomers did not dimerize with alkyl or aryl boronic acids unless supplemented with hydrogen peroxide (H2O2), which oxidatively converts boronic acids to boric acid. Real-time NMR spectroscopy and density functional theory calculations provided insight into the reaction mechanism and energetics of oxidation respectively. Together, our data show that exogenous boronic acids are a source of boric acid for plants, and that the deboronation reaction generates aryl or alkyl alcohol byproducts that can undergo further chemical modification in planta. The fate and potential roles of these byproducts in planta remain to be determined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Fatty acid foams for nonselective physical removal of microplastics from aqueous solutions

Microplastics (MPs) are pervasive environmental contaminants whose removal from water remains a major challenge due to their small size, chemical diversity, and dynamic surface properties arising from environmental aging/weathering. Here, we present a concept of foam-based separation method that physically traps MPs in the foam phase using microtubular assemblies of 12-hydroxystearic acid. These foams are stabilized by anisotropic fatty acid microtubules formed in the presence of ethanolamine, which jam within the foam channels and suppress fluid drainage thereby enhancing MP retention and foam stability. MPs of different sizes, polymer compositions (including polystyrene, polypropylene, polyethylene terephthalate, and polytetrafluoroethylene), and weathered states were retained in the foam phase without requiring chemical modification or relying on chemical interactions between the fatty acid and MPs. Thermally induced transition of the fatty acid microtubules into nanomicelles above the characteristic phase transition temperature (∼35 °C) enables controlled foam collapse and recovery of trapped MPs. The cumulative removal efficiency can exceed 85% through multiple foaming cycles, matching predictions from a probabilistic retention model. This work shows that foams can provide a simple platform to trap MPs, thus providing a new physical-removal strategy that does not rely on the particles’ chemistry.

Guillot, Kennedy A. [Louisiana State Univ., Baton ↗
DOE OSTI2026

Plasma-assisted atomic layer etching of single-crystal diamond

Applications of near-surface nitrogen-vacancy (NV) centers in diamond are often limited by surface defects created during processing. Understanding and controlling plasma-induced surface damage is important for preserving the optical and spin properties of diamond NV centers. We report molecular dynamics simulations of a novel form of plasma-aided atomic layer etching of diamond. In this proposed scheme, the initial surface modification step consists of Ar + ion bombardment. This creates an amorphous layer at the surface, the thickness of which is controlled by the ion energy. Amorphization is known to help smooth the surface, at least locally, and would also serve to sputter clean an initially contaminated surface. A second step impacts the amorphous carbon layer with O + between about 1 and 5 eV. Simulations show that this energy range will remove the amorphous carbon but will not etch the underlying diamond. Though this energy range is not trivial to achieve in a conventional low-temperature plasma, potential methods for creating these low-energy O + ions are discussed. In addition to a-C etching, the O + impacts are predicted to remove any isolated (100) diamond terraces by selectively attacking the edges of the terraces. The proposed atomic layer etching (ALE) approach reverses the conventional ALE sequence in which the surface modification step is usually chemical modification (oxidation in this case), followed by a removal step using Ar + impacts. This plasma ALE procedure is predicted to create a diamond surface that is atomically flat and defect free.

Draney, J. S. [Princeton University, NJ (United St↗
NASA NTRS1984

Neoplastic cell transformation by energetic heavy ions and its modification with chemical agents

One of the major deleterious late effects of ionizing radiation is related to the induction of neoplasms. In the present report recent experimental results on neoplastic cell transformation by heavy ions are presented, and possible means to circumvent the carcinogenic effect of space radiation are discussed. Biological effects observed in experiments involving the use of energetic heavy ions accelerated at the Bevalac suggest that many of the biological effects observed in earlier space flight experiments may be due to space radiation, particularly cosmic rays. It is found that the effect of radiation on cell transformation is dose-rate dependent. The frequency of neoplastic transformation for a given dose decreases with a decrease of dose rate of Co-60 gamma rays. It is found that various chemical agents give radiation protection, including DMSO.

Yang, T. C.↗
DOE OSTI2021

FTO regulates myoblast proliferation by controlling CCND1 expression in an m6A-YTHDF2-dependent manner

Highlights: • Silencing FTO delays cell cycle and inhibits cell proliferation. • FTO regulates cell proliferation depending on its m{sup 6}A demethylation activity. • Silencing FTO suppresses CCND1 expression via YTHDF2-mediated mRNA degradation. • Knockdown YTHDF2 eliminates the cell cycle arrest in FTO-deficient cells. N6-Methyladenosine (m{sup 6}A) modification is the most abundant chemical modification in mRNA, and it participates in various biological processes, such as cell differentiation and proliferation. However, little is known about the function of m{sup 6}A demethylase fat mass and obesity-associated (FTO) in myoblast proliferation. Here, we demonstrated that knockdown of FTO can significantly inhibit myoblast proliferation and promote apoptosis. RNA sequencing analysis revealed that a lot of downregulated genes in FTO knockdown cells are associated with cell cycle and apoptosis. Furthermore, silencing FTO drastically decreased cyclin D1 (CCND1) expression through YTHDF2-mediated mRNA degradation, thereby delaying the progression of G1 phase, and leading to impaired myoblast proliferation. These findings unraveled that FTO regulates myoblast proliferation by controlling CCND1 expression in an m{sup 6}A-YTHDF2-dependent manner, which highlights the critical roles of m{sup 6}A modification in myoblast proliferation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Materials Based on Technical Bulk Lignin

Lignin is the second most abundant biopolymer and the main source of aromatic structures on earth. Lignin has long been produced as a byproduct of the pulping process and utilized in low value-added applications like heat. However, lignin has received increased attention in recent years to improve its value through various chemical processes. This Review compiles recent progress in synthesis, properties, and applications of lignin-based materials. The lignin for material applications can often be classified into three categories: technical bulk lignin (TBL), lignin-derived oligomers (LDOs), and lignin-derived phenols (LDPs). Furthermore, this Review focuses on the chemical modifications of TBLs and their applications in novel smart materials like self-healing, stimulus responsive, and shape memory polymers. The conversion of TBL to polymers can be briefly divided into two steps: (1) introduction of polymerizable functional groups into the lignin backbone and (2) polymerization that achieves desired materials. Both lignin functionalization and polymerization approaches are discussed in detail. As such, this work attempts to provide a comprehensive overview that highlights the importance of these approaches for the utilization of the abundant but largely ignored biopolymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2007

Use of Atomic Oxygen for Increased Water Contact Angles of Various Polymers for Biomedical Applications

In the low Earth orbit (LEO) space environment, spacecraft surfaces can be altered during atomic oxygen exposure through oxidation and erosion. There can be terrestrial benefits of such interactions, such as the modification of hydrophobic or hydrophilic properties of polymers due to chemical modification and texturing. Such modification of the surface may be useful for biomedical applications. For example, atomic oxygen texturing may increase the hydrophilicity of polymers, such as chlorotrifluoroethylene (Aclar), thus allowing increased adhesion and spreading of cells on textured Petri dishes. The purpose of this study was to determine the effect of atomic oxygen exposure on the hydrophilicity of nine different polymers. To determine whether hydrophilicity remains static after atomic oxygen exposure or changes with exposure, the contact angles between the polymer and a water droplet placed on the polymer s surface were measured. The polymers were exposed to atomic oxygen in a radio frequency (RF) plasma asher. Atomic oxygen plasma treatment was found to significantly alter the hydrophilicity of non-fluorinated polymers. Significant decreases in the water contact angle occurred with atomic oxygen exposure. Fluorinated polymers were found to be less sensitive to changes in hydrophilicity for equivalent atomic oxygen exposures, and two of the fluorinated polymers became more hydrophobic. The majority of change in water contact angle of the non-fluorinated polymers was found to occur with very low fluence exposures, indicating potential cell culturing benefit with short treatment time.

Beger, Lauren↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Nanomaterial Based Sensors for NASA Missions

Nanomaterials such as carbon nanotubes (CNTs), carbon nanofibers (CNFs), graphene and metal nanowires have shown interesting electronic properties and therefore have been pursued for a variety of space applications requiring ultrasensitive and light-weight sensor and electronic devices. We have been pursuing development of chemical and biosensors using carbon nanotubes and carbon nanofibers for the last several years and this talk will present the benefits of nanomaterials these applications. More recently, printing approaches to manufacturing these devices have been explored as a strategy that is compatible to a microgravity environment. Nanomaterials are either grown in house or purchased and processed as electrical inks. Chemical modification or coatings are added to the nanomaterials to tailor the nanomaterial to the exact application. The development of printed chemical sensors and biosensors will be discussed for applications ranging from crew life support to exploration missions.

sensors↗