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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Autonomous Changes in Polymer Materials Driven by Chemical Fuels

Time-dependent properties in polymer materials can be achieved through coupling to out-of-equilibrium chemical fuel reactions that mimic biological processes. Through transient changes in bonding in polymers, transient gelation, changes in mechanical stiffness, swelling, self-healing, or self-assembly can be achieved. Recent advances in these categories are discussed. These out-of-equilibrium behaviors enable applications ranging from smart adhesives to actuators for soft robotics. However, challenges remain, including waste accumulation, bio-compatibility, and achieving functionally useful performance. Addressing these issues is essential for advancing the practical use of chemically driven polymer materials and unlocking their full potential for future technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Feature Design for Protein Interface Hotspots Using KFC2 and Rosetta

Protein–protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally characterizing protein residues that contribute the most to protein–protein interaction affinity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein–protein interfaces provides important information about how to inhibit therapeutically relevant protein–protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein–protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A two-way and three-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.

Seeger, Franziska↗
DOE OSTI2024

Beyond the Surface: Non-Invasive Low-Field NMR Analysis of Microbially-Induced Calcium Carbonate Precipitation in Shale Fractures

Microbially-induced calcium carbonate precipitation (MICP) is a biological process in which microbially-produced urease enzymes convert urea and calcium into solid calcium carbonate (CaCO 3 ) deposits. MICP has been demonstrated to reduce permeability in shale fractures under elevated pressures, raising the possibility of applying this technology to enhance shale reservoir storage safety. For this and other applications to become a reality, non-invasive tools are needed to determine how effectively MICP seals shale fractures at subsurface temperatures. In this study, two different MICP strategies were tested on 2.54 cm diameter and 5.08 cm long shale cores with a single fracture at 60 °C. Flow-through, pulsed-flow MICP-treatment was repeatedly applied to Marcellus shale fractures with and without sand (“proppant”) until reaching approximately four orders of magnitude reduction in apparent permeability, while a single application of polymer-based “immersion” MICP-treatment was applied to an Eagle Ford shale fracture with proppant. Low-field nuclear magnetic resonance (LF-NMR) and X-Ray computed microtomography (micro-CT) techniques were used to assess the degree of biomineralization. With the flow-through approach, these tools revealed that while CaCO 3 precipitation occurred throughout the fracture, there was preferential precipitation around proppant. Without proppant, the same approach led to premature sealing at the inlet side of the core. In contrast, immersion MICP-treatment sealed off the fracture edges and showed less mineral precipitation overall. This study highlights the use of LF-NMR relaxometry in characterizing fracture sealing and can help guide NMR logging tools in subsurface remediation efforts.

MICP↗
DOE OSTI2019

Long-term performance of a UASB reactor treating acid mine drainage: effects of sulfate loading rate, hydraulic retention time, and COD/SO42- ratio

Acid mine drainage (AMD) is among the most serious threats to water and the typical alkali-based treatment costs are high. This study's main objective was the establishment of a highly efficient biological process using an upflow anaerobic sludge blanket (UASB) reactor to treat AMD based on a shorter hydraulic retention time (HRT) and lower organic matter input. The process was evaluated for a long-term operation (739days) in terms of the influence of HRT (14-24h), metal addition, sulfate loading rate (0.5-2.6gSO(4)(2-)l(-1)d(-1)), and the COD/SO42- ratio (0.67-1.0) using ethanol as the only electron donor at a pH of 4.0. Neutral effluent pH was achieved throughout the time apart from operational modifications. The reduction in HRT from 24 to 16h and an increase in the sulfate loading rate (SLR) up to 2.25gSO(4)(2-)l(-1)d(-1) improved the sulfate removal to (92.1 +/- 1.8)% with 80% chemical oxygen demand (COD) removal. However, the sulfate reduction was less than 80% when the HRT and SLR was changed to 14h and 2.6gSO(4)(2-)l(-1)d(-1), respectively. The oxidation of organic matter by sulfate reduction was greater than 50% regardless of the conditions imposed but the use of ethanol to treat AMD was more efficient when either the HRT was 16h (1.5gSO(4)(2-)l(-1)d(-1)) in the presence of Fe, Zn, and Cu or the HRT was 14h (2.6gSO(4)(2-)l(-1)d(-1)) but the COD/SO42- ratio was reduced to 0.67. The fully optimized conditions of the UASB reactor were set at an HRT of 16h, SLR of 1.5gSO(4)(2-)l(-1)d(-1), and a COD/SO42- ratio of 1.0.

Acid mine drainage↗
DOE OSTI2018

Development of a Xanthene-Based Red-Emissive Fluorescent Probe for Visualizing H{sub 2}O{sub 2} in Living Cells, Tissues and Animals

Hydrogen peroxide (H{sub 2}O{sub 2}) plays important roles in the regulation of many biological processes, and the abnormal level of H{sub 2}O{sub 2} has close relation with the initiation and progression of many diseases. Herein, we describe a novel red-emissive fluorescence probe (RhoB) for the visualization of H{sub 2}O{sub 2} in living cells, tissues and animals. RhoB was constructed on the basis of a xanthene-based red-emissive dye, and displayed nearly no fluorescence. After the treatment with H{sub 2}O{sub 2}, RhoB can exhibit red fluorescence with the emission wavelength at 638 nm. RhoB exhibited highly sensitive and selective response to H{sub 2}O{sub 2}. Density functional theory (DFT) calculations were conducted to shed light on the optical properties of RhoB, and natural bond orbital (NBO) calculations demonstrate that the boron atom shows the highest positive electricity and further support the response mechanism. RhoB was successfully applied for imaging of exogenous and endogenous H{sub 2}O{sub 2} in living cells, and also can be utilized for visualizing H{sub 2}O{sub 2} in living tissues and animals.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Role of Interactions and Correlations on Collective Dynamics of Molecular Motors Along Parallel Filaments

Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest molecules of their filament while performing any mechanical work. These interactions modify the microscopic level properties of motor proteins. In this work, a new version of two-channel totally asymmetric simple exclusion process, that incorporates the intra-channel interactions in a thermodynamically consistent way, is proposed. As the existing approaches for multi-channel systems deviate from analyzing the combined effect of inter and intra-channel interactions, a new approach known as modified vertical cluster mean field is developed. The approach along with Monte Carlo simulations successfully encounters some correlations and computes the complex dynamic properties of the system. Role of symmetry of interactions and inter-channel coupling is observed on the phase diagrams, maximal particle current and its corresponding optimal interaction strength. Surprisingly, for all values of coupling rate and most of the interaction splittings, the optimal interaction strength corresponding to maximal current belongs to the case of weak repulsive interactions. Moreover, for weak interaction splittings and with an increase in the coupling rate, the optimal interaction strength tends towards the known experimental results. The effect of coupling as well as interaction energy is also measured for correlations. They are found to be short-range and weaker for repulsive and weak attractive interactions while they are long-range and stronger for large attractions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Identification of important invasion and proliferation related genes in adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is an end‐stage hormonal syndrome. Although profound attempts have been made to illuminate the pathogenesis, the molecular mechanisms of ACC remain to be clarified. To identify the important genes in the progression of ACC, microarray datasets GSE19775 was downloaded from the gene expression omnibus database. The differentially-expressed genes (DEGs) were identified, and pathway and GO enrichment analyses were performed. The protein–protein interaction (PPI) network was constructed and the module analysis was performed using the protein interaction network analysis and Cytoscape. Also constructed target genes–miRNA regulatory network and target genes–TF regulatory network. Correlation of the hub genes were analyzed in The Cancer Genome Atlas. The prognostic values of hub genes were further validated by online tool UALCAN. Mutation analysis was done by online tool CBio Cancer Genomics Portal. A total of 884 DEGs were identified, with 441 in up regulation and 443 in down regulation. Pathways in catecholamine biosynthesis, aldosterone synthesis and secretion, pyrimidine deoxyribonucleosides salvage and systemic lupus erythematosus were the most significantly enriched for DEGs (up and down regulated). Blood vessel morphogenesis and cell cycle phase transition were the most significantly enriched term in biological processes, while extracellular matrix and chromosome, centromeric region were in cellular component and heparin binding and protein dimerization activity were in molecular function. Among the PPI networks and its module, target genes–miRNA regulatory network and target genes–TF regulatory network, hub genes were YWHAZ, FN1, GRK5, VCAM1, GATA6, TXNIP, HSPA1A, and F11R. Hub genes such as YWHAZ, STAT1, ICAM1, SH3BP5, CD83, FN1, TK1, HIST1H1C, CABLES1, and MCM3 were associated with poor overall survival, while hub genes such as STAT1, ICAM1, CD83, FN1, TK1, HIST1H1C, and MCM3 were highly expressed in stage 4. In conclusion, DEGs and hub genes diagnosed in this study may deepen our understanding of molecular mechanisms underlying the progression of ACC, and provide important targets for diagnosis and treatment of ACC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

CMPLE: Correlation Modeling to Decode Photosynthesis Using the Minorize–Maximize Algorithm

In plant genomic experiments, correlations among various biological traits (phenotypes) give new insights into how genetic diversity may have tuned biological processes to enhance fitness under diverse conditions. Consequently, knowing how the correlations are affected by genetic (G) and environmental (E) factors helps develop climate-resilient plants. However, the current literature lacks any method for assessing the effect of predictors on pairwise correlations among multiple phenotypes together with easily interpretable model parameters. To address this need, we propose to model pairwise correlations directly in terms of G and E and develop a computationally efficient inference procedure. Two major novelties in our methodology are (1) the use of a composite pairwise likelihood method to avoid the positive definiteness restriction on the correlation matrix and (2) the use of a novel Minorize–Maximize (MM) algorithm for the efficient estimation of a large number of parameters. The proposed method shows excellent numerical performance on synthetic datasets. Here, the analysis of the motivating data on cowpea reveals that the rates of solar energy storage by photosynthesis (the aggregate trait) are differentially affected by different genetic loci through two distinct processes: “photoinhibition” which results from photodamage caused by excess light, and “photoprotection” which protects plants from photodamage but also results in energy loss.

Correlation modeling↗
DOE OSTI2017

Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment

Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analysis by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Investigation of the Ionization Mechanism of NAD{sup +}/NADH-Modified Gold Electrodes in ToF-SIMS Analysis

Analysis of nicotinamide adenine dinucleotide (NAD{sup +}/NADH)-modified electrodes is important for in vitro monitoring of key biological processes. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze NAD{sup +}/NADH-modified gold electrodes. Interestingly, no obvious characteristic peaks of nicotinamide fragment could be observed in the mass spectra of NAD{sup +}/NADH in their neutral sodium pyrophosphate form. However, after acidification, the characteristic peaks for both NAD{sup +} and NADH were detected. This was due to the suppression effect of inner pyrophosphoric salts in both neutral molecules. Besides, it was proved that the suppression by inner salt was intramolecular. No obvious suppression was found between neighboring molecules. These results demonstrated the suppression effect of inner salts in ToF-SIMS analysis, providing useful evidence for the study of ToF-SIMS ionization mechanism of organic molecule-modified electrodes. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Integrating continuous atmospheric boundary layer and tower-based flux measurements to advance understanding of land-atmosphere interactions

The atmospheric boundary layer mediates the exchange of energy, matter, and momentum between the land surface and the free troposphere, integrating a range of physical, chemical, and biological processes and is defined as the lowest layer of the atmosphere (ranging from a few meters to 3 km). In this review, we investigate how continuous, automated observations of the atmospheric boundary layer can enhance the scientific value of co-located eddy covariance measurements of land-atmosphere fluxes of carbon, water, and energy, as are being made at FLUXNET sites worldwide. We highlight four key opportunities to integrate tower-based flux measurements with continuous, long-term atmospheric boundary layer measurements: (1) to interpret surface flux and atmospheric boundary layer exchange dynamics and feedbacks at flux tower sites, (2) to support flux footprint modelling, the interpretation of surface fluxes in heterogeneous terrain, and quality control of eddy covariance flux measurements, (3) to support regional-scale modeling and upscaling of surface fluxes to continental scales, and (4) to quantify land-atmosphere coupling and validate its representation in Earth system models. Adding a suite of atmospheric boundary layer measurements to eddy covariance flux tower sites, and supporting the sharing of these data to tower networks, would allow the Earth science community to address new emerging research questions, better interpret ongoing flux tower measurements, and would present novel opportunities for collaborations between FLUXNET scientists and atmospheric and remote sensing scientists.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Design and synthesis of astatinated benzothiazole compounds for their potential use in Targeted Alpha Therapy (TAT) strategies to treat Alzheimer's disease-associated amyloid plaques

Alzheimer's disease (AD) is a terminal neurodegenerative disease characterized by the buildup of amyloid fibrils, amorphous aggregates and tauopathies. Several treatment modalities, which rely on various biological processes to reduce disease burden, have been largely ineffective at treating Alzheimer's disease. Targeted alpha therapy (TAT) has demonstrated positive results in the treatment of cancer. Benzothiazole derivatives have been successfully shown to target these plaques and are used in several imaging applications. One such derivative, Flutemetamol (Vizamyl TM ) is an FDA approved diagnostic tool for PET imaging of AD-associated plaques. We report the radiolabeling of benzothiazole derivatives with 211 At, a 7.2 h alpha emitting radionuclide, using a copper catalyzed reaction with a boronic acid precursor molecule. In conclusion, our final compound [ 211 At]3'-At-PIB-OMe had a radiochemical yield of 55% and was found to be stable for at least 3 h in phosphate buffered saline.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

tRNA modification profiles of the fast-proliferating cancer cells

Despite the recent progress in RNA modification study, a comprehensive modification profile is still lacking for mammalian cells. Using a quantitative HPLC/MS/MS assay, we present here a study where RNA modifications are examined in term of the major RNA species. With paired slow- and fast-proliferating cell lines, distinct RNA modification profiles are first revealed for diverse RNA species. Compared to mRNAs, increased ribose and nucleobase modifications are shown for the highly-structured tRNAs and rRNAs, lending support to their contribution to the formation of high-order structures. This study also reveals a dynamic tRNA modification profile in the fast-proliferating cells. In addition to cultured cells, this unique tRNA profile has been further confirmed with endometrial cancers and their adjacent normal tissues. Taken together, the results indicate that tRNA is a actively regulated RNA species in the fast-proliferating cancer cells, and suggest that they may play a more active role in biological process than expected. -- Highlights: •RNA modifications were first examined in term of the major RNA species. •A dynamic tRNA modifications was characterized for the fast-proliferating cells. •The unique tRNA profile was confirmed with endometrial cancers and their adjacent normal tissues. •tRNA was predicted as an actively regulated RNA species in the fast-proliferating cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

CHIP promotes thyroid cancer proliferation via activation of the MAPK and AKT pathways

The carboxyl terminus of Hsp70-interacting protein (CHIP) is a U box-type ubiquitin ligase that plays crucial roles in various biological processes, including tumor progression. To date, the functional mechanism of CHIP in thyroid cancer remains unknown. Here, we obtained evidence of upregulation of CHIP in thyroid cancer tissues and cell lines. CHIP overexpression markedly enhanced thyroid cancer cell viability and colony formation in vitro and accelerated tumor growth in vivo. Conversely, CHIP knockdown impaired cell proliferation and tumor growth. Notably, CHIP promoted cell growth through activation of MAPK and AKT pathways, subsequently decreasing p27 and increasing cyclin D1 and p-FOXO3a expression. Our findings collectively indicate that CHIP functions as an oncogene in thyroid cancer, and is therefore a potential therapeutic target for this disease. - Highlights: • CHIP is significantly upregulated in thyroid cancer cells. • Overexpression of CHIP facilitates proliferation and tumorigenesis of thyroid cancer cells. • Silencing of CHIP inhibits the proliferation and tumorigenesis of thyroid cancer cells. • CHIP promotes thyroid cancer cell proliferation via activating the MAPK and AKT pathways.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Geranylgeranyl pyrophosphate performs as an endogenous regulator of adipocyte function via suppressing the LXR pathway

Isoprenoids such as geranylgeranyl pyrophosphate (GGPP) influence various biological processes. Here we show that GGPP inhibits adipocyte differentiation via the liver X receptors (LXRs) pathway. Intracellular GGPP levels and GGPP synthase (Ggps) mRNA expression increases during adipocyte differentiation. Ggps expression also increases in white adipose tissue of obese mice. GGPP addition reduces the expression of adipogenic marker genes such as adipocyte fatty acid binding protein, peroxisome proliferator-activated receptor γ, and insulin-stimulated glucose uptake. Similarly, over-expressing Ggps inhibits adipocyte differentiation. In contrast, Ggps knockdown promotes adipocyte differentiation. Inhibition of adipocyte differentiation by GGPP was partially reduced by LXR agonist T0901317. Furthermore, Ggps knockdown up-regulates LXR target genes during adipocyte differentiation. These results suggest that GGPP may act as an endogenous regulator of adipocyte differentiation and maturation through a mechanism partially dependent on the LXR pathway. - Highlights: • Intracellular GGPP levels are enhanced during adipocyte differentiation. • GGPP suppresses adipocyte differentiation and maturation. • The inhibitory effects of GGPP are partially through the LXRs signaling pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

microRNA-146a inhibits proliferation, migration and invasion of human cervical and colorectal cancer cells

microRNAs (miRNAs) play significant roles in diverse biological processes and their deregulation is implicated in carcinogenesis. miR-146a executes tumour suppressive or oncogenic functions depending on the cancer type, but its effect on human cervical (CaCx) and colorectal (CRC) cancers have not been examined thus far. In this study, miR-146a exhibited high expression in CaCx but poor expression in CRC, in comparison to corresponding normal tissues. Nevertheless, ectopic expression of miR-146a inhibited proliferation in both CaCx and CRC cells and curbed their migration and invasion. When the expression of endogenous miR-146a was suppressed, proliferative, migratory and invasive capacities of CaCx and CRC cells increased, suggesting an anti-tumourigenic function for miR-146a. Re-expression of miR-146a down-regulated the expression of crucial signalling intermediates: CTNNB1, STAT3, RELA, CCND1 and SNAI1, and enhanced TP53 and CDH1 expression. Thus, the present study reveals a hitherto unknown tumour suppressive role for miR-146a providing a plausible mechanistic basis for it. - Highlights: • miR-146a inhibits proliferation in human cervical and colorectal cancer cells. • miR-146a retards migratory and invasive potentials of cancer cells. • AntimiR-146a enhances growth and motility. • miR-146a modulates the expression of a few genes related to growth and motility. • miR-146a is highly expressed in cervical but poorly so in colorectal tumours.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Rock2 promotes RCC proliferation by decreasing SCARA5 expression through β-catenin/TCF4 signaling

Rho-associated coiled-coil forming protein kinase 2 (Rock2), as a key effector of the small GTPase RhoA, is involved in tumor development. Scavenger receptor class A member 5 (SCARA5) is an important regulator of biological processes in cancer cells. However, the roles and relationship of Rock2 and SCARA5 in renal cell carcinoma (RCC) remain unclear. In this study, we found that Rock2 expression was markedly increased in clinical RCC tissues compared with that in adjacent non-cancerous tissues. High expression of Rock2 was inversely correlated with patient survival in RCC, which indicated that Rock2 may be a prognostic marker in human RCC. In addition, Rock2 knockdown increased SCARA5 expression and suppressed RCC cell proliferation both in vitro and in vivo. Furthermore, we found that the β-catenin/TCF4 pathway contributed to the effect of Rock2 on SCARA5-mediated RCC proliferation. Taken together, these results suggest that this newly identified Rock2-β-catenin/TCF4-SCARA5 axis will provide novel insight into the understanding of the regulatory mechanisms of proliferation in human RCC. - Highlights: • Rock2 is overexpressed in RCC. • Rock2 may be considered a prognostic marker in human RCC. • Rock2 influences RCC proliferation by regulating SCARA5 expression. • Rock2 regulates SCARA5 expression via the β-catenin/TCF4 pathway.

60 APPLIED LIFE SCIENCES↗