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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Derivatization of Mirror-Image L -Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization

To further expand the functionality and enhance the stability of mirror-image nucleic acids as advanced agents for basic research and therapeutic design, we have synthesized 2'-deoxy-2'-methoxy- L -uridine phosphoramidite and incorporated it into L -DNA and L -RNA by solid-phase synthesis quantitatively. We found that the thermostability of L -nucleic acids is dramatically improved after introducing the modifications. Moreover, we successfully crystallized both L -DNA and L -RNA duplexes containing the 2'-OMe modifications and sharing identical sequences. Crystal structure determination and analysis revealed the overall structures of the mirror-image nucleic acids, and for the first time it was possible to interpret the structural deviations caused by 2'-OMe and 2'-OH groups in the oligonucleotides, which are very similar. In conclusion, this novel chemical nucleic acid modification has the potential to be used to design nucleic acid-based therapeutics and materials in the future.

2'-OMe-modifications↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2019

Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction–modification systems

A major barrier to both metabolic engineering and fundamental biological studies is the lack of genetic tools in most microorganisms. One example is Clostridium thermocellum ATCC 27405 T , where genetic tools are not available to help validate decades of hypotheses. A crucial barrier to DNA transformation is restriction–modification systems, which defend against foreign DNA methylated differently than the host. To determine the active restriction–modification systems in this strain, we performed complete methylome analysis via single-molecule, real-time sequencing to detect 6-methyladenine and 4-methylcytosine and the rarely used whole-genome bisulfite sequencing to detect 5-methylcytosine. Multiple active systems were identified, and corresponding DNA methyltransferases were expressed from the Escherichia coli chromosome to mimic the C. thermocellum methylome. Plasmid methylation was experimentally validated and successfully electroporated into C. thermocellum ATCC 27405. This combined method enabled genetic modification of the C. thermocellum -type strain and acts as a blueprint for transformation of other non-model microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

An Investigation of Process Parameter Modifications on Additively Manufactured Inconel 718 Parts

Additive manufacturing (AM) allows for the fabrication of complex parts via layer-by-layer melting of metal powder. Laser powder-bed AM processes use a variety of process parameters including beam power, beam velocity, and hatch spacing to control melting. Alterations to these parameters have often been attempted to reduce porosity, for example, but less work has been done to on comprehensive effects of process parameter modifications. This study looks at the effects of altering these parameters on microstructure, porosity, and mechanical performance of Inconel 718. The results showed that process parameter modifications that result in porosity formation can significantly reduce fatigue life, while microstructure changes were minimal and had little effect on tensile properties. The precipitate structure was not found to be changed significantly. These results can inform future process parameter modifications, as well as heat treatments to optimize mechanical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2017

CACUL1/CAC1 attenuates p53 activity through PML post-translational modification

Promyelocytic leukaemia (PML) is a tumor suppressor protein covalently conjugated with SUMO family proteins, leading to the formation of PML nuclear bodies (NBs). PML-NBs provide a platform for efficient posttranslational modification of targets and protein-protein interaction, contributing to the adjustment of gene expression and chromatin integrity. Although PML SUMOylation is thought to play important roles in diverse cellular functions, the control mechanisms of adequate modification levels have remained unsolved. Here, we report that Cullin-related protein CACUL1/CAC1 (CACUL1) inhibits PML posttranslational modification. CACUL1 interacts with PML and suppresses PML SUMOylation, leading to the regulation of PML-NB size in the nucleus. We also found that Ubc9, a SUMO-conjugating enzyme, binds to CACUL1 and antagonizes the interaction between CACUL1 and PML. Furthermore, CACUL1 attenuates p53 transcriptional activity. These data suggest that CACUL1 is a novel regulator that negatively controls p53 activity through the regulation of PML SUMOylation. - Highlights: • CACUL1 suppresses PML SUMOylation. • CACUL1 regulates PML-NBs size. • CACUL1 attenuates p53 transcriptional activity.

43 PARTICLE ACCELERATORS↗
DOE OSTI2015

Atom-scale covalent electrochemical modification of single-layer graphene on SiC substrates by diaryliodonium salts

Owing to its high conductivity, graphene holds promise as an electrode for energy devices such as batteries and photovoltaics. However, to this end, the work function and doping levels in graphene need to be precisely tuned. One promising route for modifying graphene’s electronic properties is via controlled covalent electrochemical grafting of molecules. We show that by employing diaryliodonium salts instead of the commonly used diazonium salts, spontaneous functionalization is avoided. This then allows for precise tuning of the grafting density. Moreover, by employing bis(4-nitrophenyl)iodonium(III) tetrafluoroborate (DNP) salt calibration curves, the surface functionalization density (coverage) of glassy carbon was controlled using cyclic voltammetry in varying salt concentrations. These electro-grafting conditions and calibration curves translated directly over to modifying single layer epitaxial graphene substrates (grown on insulating 6H-SiC (0 0 0 1)). In addition to quantifying the functionalization densities using electrochemical methods, samples with low grafting densities were characterized by low-temperature scanning tunneling microscopy (LT-STM). We show that the use of buffer-layer free graphene substrates is required for clear observation of the nitrophenyl modifications. Furthermore, atomically-resolved STM images of single site modifications were obtained, showing no preferential grafting at defect sites or SiC step edges as supposed previously in the literature. Most of the grafts exhibit threefold symmetry, but occasional extended modifications (larger than 4 nm) were observed as well.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Deoxynivalenol exposure induces autophagy/apoptosis and epigenetic modification changes during porcine oocyte maturation

Deoxynivalenol (DON) is a widespread trichothecene mycotoxin which contaminates agricultural staples and elicits a complex spectrum of toxic effects on humans and animals. It has been shown that DON impairs oocyte maturation, reproductive function and causes abnormal fetal development in mammals; however, the mechanisms remain unclear. In the present study, we investigate the possible reasons of the toxic effects of DON on porcine oocytes. Our results showed that DON significantly inhibited porcine oocyte maturation and disrupted meiotic spindle by reducing p-MAPK protein level, which caused retardation of cell cycle progression. In addition, up-regulated LC3 protein expression and aberrant Lamp2, LC3 and mTOR mRNA levels were observed with DON exposure, together with Annexin V-FITC staining assay analysis, these results indicated that DON treatment induced autophagy/apoptosis in porcine oocytes. We also showed that DON exposure increased DNA methylation level in porcine oocytes through altering DNMT3A mRNA levels. Histone methylation levels were also changed showing with increased H3K27me3 and H3K4me2 protein levels, and mRNA levels of their relative methyltransferase genes, indicating that epigenetic modifications were affected. Taken together, our results suggested that DON exposure reduced porcine oocytes maturation capability through affecting cytoskeletal dynamics, cell cycle, autophagy/apoptosis and epigenetic modifications. - Highlights: • DON exposure disrupted meiotic spindle by reducing p-MAPK expression. • DON exposure caused retardation of cell cycle progression in porcine oocytes. • DON triggered autophagy and early-apoptosis in porcine oocytes. • DON exposure led to aberrant epigenetic modifications in porcine oocytes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. In this paper, we present an analytical workflow to explore the changes in histone modifications through plant developmental stages and two drought stresses in two sorghum genotypes that differ in their response to drought. Top-down mass spectrometry (MS) is an ideal method to profile histone modifications and distinguish closely related histone proteoforms. We analyzed leaves of 48 plants and identified 26 unique histone proteins and 677 unique histone proteoforms (124 full-length and 553 truncated proteoforms). We detected trimethylation on nearly all H2B N-termini where acetylation is commonly expected. In addition, an unexpected modification on H2A histones was assigned to N-pyruvic acid 2-iminylation based on its unique neutral loss of CO 2 . Interestingly, some of the truncated histones, in particular H4 and H3.2, showed significant changes that correlated with the growth and water conditions. Furthermore, the histone proteoforms could serve as targets in search of chromatin modifiers and ultimately have important ramifications in future attempts of studying plant epigenetic reprogramming under stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore

Various proteoforms may be generated from a single gene due to primary structure alterations (PSAs) such as genetic variations, alternative splicing, and post-translational modifications (PTMs). Top-down mass spectrometry is capable of analyzing intact proteins and identifying patterns of multiple PSAs, making it the method of choice for studying complex proteoforms. In top-down proteomics, proteoform identification is often performed by searching tandem mass spectra against a protein sequence database that contains only one reference protein sequence for each gene or transcript variant in a proteome. Because of the incompleteness of the protein database, an identified proteoform may contain unknown PSAs compared with the reference sequence. Proteoform characterization is to identify and localize PSAs in a proteoform. Although many software tools have been proposed for proteoform identification by top-down mass spectrometry, the characterization of proteoforms in identified proteoform-spectrum matches still relies mainly on manual annotation. We propose to use the Modification Identification Score (MIScore), which is based on Bayesian models, to automatically identify and localize PTMs in proteoforms. Experiments showed that the MIScore is accurate in identifying and localizing one or two modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines

Protein cysteine thiols play a crucial role in redox signaling, regulation of enzymatic activity and protein function, and maintaining redox homeostasis in living systems. The unique chemical reactivity of thiol groups makes cysteine susceptible to oxidative modifications by reactive oxygen and nitrogen species to form a broad array of reversible and irreversible protein post-translational modifications (PTMs). The reversible modifications in particular are one of the major components of redox signaling and are involved in regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in health and diseases has been increasingly recognized. Herein, we review the recent advances of quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including the general considerations of sample processing, various chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for addressing specific biological questions. Although some technological limitations remain, redox proteomics is paving the way towards a better understanding of redox signaling and regulation in human health and diseases.

Cysteine↗
DOE OSTI2014

Tuning electron transport through a single molecular junction by bridge modification

The possibility of controlling electron transport in a single molecular junction represents the ultimate goal of molecular electronics. Here, we report that the modification of bridging group makes it possible to improve the performance and obtain new functions in a single cross-conjugated molecular junction, designed from a recently synthesized bipolar molecule bithiophene naphthalene diimide. Our first principles results show that the bipolar characteristic remains after the molecule was modified and sandwiched between two metal electrodes. Rectifying is the intrinsic characteristic of the molecular junction and its performance can be enhanced by replacing the saturated bridging group with an unsaturated group. A further improvement of the rectifying and a robust negative differential resistance (NDR) behavior can be achieved by the modification of unsaturated bridge. It is revealed that the modification can induce a deviation angle about 4° between the donor and the acceptor π-conjugations, making it possible to enhance the communication between the two π systems. Meanwhile, the low energy frontier orbitals of the junction can move close to the Fermi level and encounter in energy at certain biases, thus a transport channel with a considerable transmission can be formed near the Fermi level only at a narrow bias regime, resulting in the improvement of rectifying and the robust NDR behavior. This finding could be useful for the design of single molecular devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2014

The influence of molecular interface modification on the charge dynamics of polymeric semiconductor:ZnO heterostructure

We demonstrate an enhancement of photocurrent in hybrid photovoltaic cells based on nanoparticles of zinc oxide (ZnO) and poly(3-hexylthiophene) (P3HT), through molecular interface modification with and without cis-bis(4,4′-dicarboxy-2,2′bipyridine) ruthenium (II) (N3-dye) and α-Sexithiophen-2-yl-phosphonic Acid (6TP) as interface modifiers. We identify the formation of long-lived polarons at P3HT:ZnO interface by means of quasi-steady-state photoinduced absorption (PIA) spectroscopy. Furthermore, by probing the pump-modulation-frequency-dependent PIA signal, we find that P3HT:ZnO-N3 and P3HT:ZnO-6TP exhibit more sharply decaying density with increasing modulation frequency, which is indicative of a longer average lifetime, approximating 1 ms as opposed to ∼0.2 ms without ZnO surface modification. This highlights the importance of the molecular interface modification in the steady-state polaron dynamics in hybrid solar cells.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Modification of cellulose acetate nanocomposite with TiO{sub 2}-organoclay as nanofiller and its self-photodegradation study

Nanocomposite cellulose acetate has been synthesized using organoclay nanofiller modified with TiO{sub 2}. Tapanuli bentonite was previously subjected to purification and sodium exchangeprocesses, then modified with TiO{sub 2},that was added as much as 0%, 1%, 3%, 5%, and 10% weight of the total composite. FTIR analysis showed intercalation with Hexadecyl Ammonium Bromide (HDTMABr) surfactant was successfully carried out, indicated by new absorption bands at 2636 cm{sup −1} and 2569 cm{sup −1}. XRD diffractogram shows the increase in basal spasing on the modification of bentonite from 15.7 Å to 19.7 Å after modification. Fabrication of nanocomposite film was carried out using acetone as solvent and through solvent casting method. Nanocomposite application in photodegradation test was carried out under direct sunlight irradiation, UV light, and without irradiation for six days. It is found that the greater the amount of TiO{sub 2} in the composites, the more weight loss occured, due to photodegredation. Percent weight loss in the UV light irradiation are 1.11%, 2.15%, 2.73%, 3.18%, and 3.96%, while under direct sunlight irradiation, the weight loss was 1.03%, 3.03%, 3.88%, 4.53%, and 5.57%. Modification of nanocomposite with the addition of photocatalytic TiO{sub 2} has shown to give the nanocomposite the ability of self-photodegradation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Modification of a new polymer photorecording material based on PMMA doped with 2,2-difluoro-4-(9-antracyl)-6-methyl-1,3,2-dioxaborine by ultrashort pulses

Specific features of modification of a new photorecording material based on PMMA doped with 2,2-difluoro-4-(9-antracyl)-6-methyl-1,3,2-dioxaborine are studied. The recording of the filament distribution in the studied material occurs at the expense of two-photon photochemical processes. The three-dimensional modification of the material is achieved in the filamentation regime without supercontinuum generation. It is possible to order the volume structure by preliminary photo-modification of the near-surface layer of the material. (extreme light fields and their applications)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

Regulated gene expression controls organismal development, and variation in regulatory patterns has been implicated in complex traits. Thus accurate prediction of enhancers is important for further understanding of these processes. Genome-wide measurement of epigenetic features, such as histone modifications and occupancy by transcription factors, is improving enhancer predictions, but the contribution of these features to prediction accuracy is not known. Given the importance of the hematopoietic transcription factor TAL1 for erythroid gene activation, we predicted candidate enhancers based on genomic occupancy by TAL1 and measured their activity. Contributions of multiple features to enhancer prediction were evaluated based on the results of these and other studies. Results: TAL1-bound DNA segments were active enhancers at a high rate both in transient transfections of cultured cells (39 of 79, or 56%) and transgenic mice (43 of 66, or 65%). The level of binding signal for TAL1 or GATA1 did not help distinguish TAL1-bound DNA segments as active versus inactive enhancers, nor did the density of regulation-related histone modifications. A meta-analysis of results from this and other studies (273 tested predicted enhancers) showed that the presence of TAL1, GATA1, EP300, SMAD1, H3K4 methylation, H3K27ac, and CAGE tags at DNase hypersensitive sites gave the most accurate predictors of enhancer activity, with a success rate over 80% and a median threefold increase in activity. Chromatin accessibility assays and the histone modifications H3K4me1 and H3K27ac were sensitive for finding enhancers, but they have high false positive rates unless transcription factor occupancy is also included. Conclusions: Occupancy by key transcription factors such as TAL1, GATA1, SMAD1, and EP300, along with evidence of transcription, improves the accuracy of enhancer predictions based on epigenetic features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Effects of Heterologous tRNA Modifications on the Production of Proteins Containing Noncanonical Amino Acids

Synthesis of proteins with noncanonical amino acids (ncAAs) enables the creation of protein-based biomaterials with diverse new chemical properties that may be attractive for material science. Current methods for large-scale production of ncAA-containing proteins, frequently carried out in Escherichia coli, involve the use of orthogonal aminoacyl-tRNA synthetases (o-aaRSs) and tRNAs (o-tRNAs). Although o-tRNAs are designed to be orthogonal to endogenous aaRSs, their orthogonality to the components of the E. coli metabolism remains largely unexplored. We systematically investigated how the E. coli tRNA modification machinery affects the efficiency and orthogonality of o-tRNASep used for production of proteins with the ncAA O-phosphoserine (Sep). The incorporation of Sep into a green fluorescent protein (GFP) in 42 E. coli strains carrying deletions of single tRNA modification genes identified several genes that affect the o-tRNA activity. Deletion of cysteine desulfurase (iscS) increased the yield of Sep-containing GFP more than eightfold, while overexpression of dimethylallyltransferase MiaA and pseudouridine synthase TruB improved the specificity of Sep incorporation. These results highlight the importance of tRNA modifications for the biosynthesis of proteins containing ncAAs, and provide a novel framework for optimization of o-tRNAs.

aminoacyl-tRNA synthetases↗
DOE OSTI2020

Aqueous Polymer Modification of Cellulose Nanofibrils by Grafting‐Through a Reactive Methacrylate Group

Abstract Modifying the surface of cellulose nanofibrils (CNFs) produced by mechanical refinement with a variety of polymer functional groups in an entirely water‐based system is challenging because only surface hydroxyl groups are accessible. To address this limitation, an entirely water‐based, polymer modification scheme is developed. CNFs are functionalized with a reactive methacrylate functional group followed by subsequent grafting‐through polymerization. This modification worked with a variety of water‐soluble and water‐insoluble (meth)acrylates and (meth)acrylamides, grafting up to 45 wt% polymer on to the CNFs. The reaction conditions introducing the methacrylate functional group are adjusted to vary the degree of functionality. Soxhlet extraction of modified samples demonstrates that the reactive methacrylate group is necessary to facilitate polymer grafting. The degree of functionalization of the polymers is studied via quantitative transmission IR spectroscopy and the morphology of the resulting cellulose nanofibrils is studied via a combination of optical, scanning electron, and atomic force microscopy. High levels of polymer modification do not significantly affect the micrometer‐scale fibril morphology.

Kelly, Peter V.↗
DOE OSTI2018

Medium modification of the shape of small-radius jets in central Pb-Pb collisions at $\sqrt{s_{\mathrm{NN}}}=2.76$ TeV

We present the measurement of a new set of jet shape observables for track-based jets in central Pb-Pb collisions at $\sqrt{s_{\mathrm{NN}}}=2.76$ TeV. The set of jet shapes includes the first radial moment or angularity, g; the momentum dispersion, pTD; and the difference between the leading and sub-leading constituent track transverse momentum, LeSub. These observables provide complementary information on the jet fragmentation and can constrain different aspects of the theoretical description of jet-medium interactions. The jet shapes were measured for a small resolution parameter R = 0.2 and were fully corrected to particle level. The observed jet shape modifications indicate that in-medium fragmentation is harder and more collimated than vacuum fragmentation as obtained by PYTHIA calculations, which were validated with the measurements of the jet shapes in proton-proton collisions at $\sqrt{s}=7$ TeV. The comparison of the measured distributions to templates for quark and gluon-initiated jets indicates that in-medium fragmentation resembles that of quark jets in vacuum. We further argue that the observed modifications are not consistent with a totally coherent energy loss picture where the jet loses energy as a single colour charge, suggesting that the medium resolves the jet structure at the angular scales probed by our measurements (R = 0.2). Furthermore, we observe that small-R jets can help to isolate purely energy loss effects from other effects that contribute to the modifications of the jet shower in medium such as the correlated background or medium response.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗