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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Facile synthesis of the nitrogen-doped graphene quantum dots at low temperature for cellular labeling

Highlights: • The N-GQDs are prepared via a facile stirring method on a magnetic stirrer at low temperature. • The N-GQDs exhibit outstanding biocompatibility in the live HeLa cells for biological applications. • The live cells keep a 100% survival rate in the high N-GQDs concentration of 200 μg mL{sup −1} for 48 h. - Abstract: A facile one-step approach is developed for the large-scale synthesis of nitrogen doped graphene quantum dot (N-GQDs) at low temperature by using citric acid (CA) as the precursor. The emission wavelength of the N-GQDs is nearly excitation-dependent, which may mirror the effects from particles of different sizes and distribution of different emissive sites on nanoparticles. Moreover, the products are then tested with live Hela cells for the extraordinary biocompatibility. The cellular viability is remained to be 100% even after a 48 h exposure with the high N-GQDs concentration of 200 μg mL{sup −1} and this survival rate is really much higher than that have been reported previously. The as-prepared N-GQDs with negligible inherent toxicity exhibit excellent biological applications such as bio-imaging and cell tracking.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Directionally supervised cellular automaton for the initial peopling of Sahul

Reconstructing the patterns of Homo sapiens expansion out of Africa and across the globe has been advanced using demographic and travel-cost models. However, modelled routes are ipso facto influenced by migration rates, and vice versa. We combined movement ‘superhighways’ with a demographic cellular automaton to predict one of the world's earliest peopling events — Sahul between 75000 and 50000 years ago. Novel outcomes from the superhighways-weighted model include (i) an approximate doubling of the predicted time to continental saturation (~10,000 years) compared to that based on the directionally unsupervised model (~5000 years), suggesting that rates of migration need to account for topographical constraints in addition to rate of saturation; (ii) a previously undetected movement corridor south through the centre of Sahul early in the expansion wave based on the scenarios assuming two dominant entry points into Sahul; and (iii) a better fit to the spatially de-biased, Signor-Lipps-corrected layer of initial arrival inferred from dated archaeological material. Our combined model infrastructure provides a data-driven means to examine how people initially moved through, settled, and abandoned different regions of the globe.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Art and Science of the Cellular Mesoscale

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Long noncoding RNAs: A potential target in sepsis-induced cellular disorder

Sepsis, an inflammation-related clinical syndrome, is characterized by disrupted immune homeostasis accompanied by infection and multiple organ dysfunction as determined by the Sequential Organ Failure Assessment (SOFA). Substantial evidence has recently suggested that lncRNAs orchestrate various biological processes in diseases, and lncRNAs play special roles in the diagnosis and management of sepsis. To date, very few reviews have provided clear and comprehensive clues to demonstrate the roles of lncRNAs in the pathogenesis of sepsis. Based on previously published studies, in this review, we summarize the different functions of lncRNAs in sepsis-induced cellular disorders and sepsis-induced organ failure to show the potential roles of lncRNAs in the diagnosis and management of sepsis. We further depict the function of some lncRNAs known to be pivotal regulators in the pathogenesis of sepsis to discuss the underlying molecular events. Additionally, we list and discuss several hotspots in research on lncRNAs, which may be conducive to future lncRNA-targeted therapeutic approaches for sepsis treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity

Cyanobacterial carboxysomes encapsulate carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Genetic deletion of the major structural proteins encoded within the ccm operon in Synechococcus sp. PCC 7002 ( ΔccmKLMN ) disrupts carboxysome formation and significantly affects cellular physiology. In this study, we employed both metabolite pool size analysis and isotopically nonstationary metabolic flux analysis (INST-MFA) to examine metabolic regulation in cells lacking carboxysomes. Under high CO 2 environments (1%), the ΔccmKLMN mutant could recover growth and had a similar central flux distribution as the control strain, with the exceptions of moderately decreased photosynthesis and elevated biomass protein content and photorespiration activity. Metabolite analyses indicated that the ΔccmKLMN strain had significantly larger pool sizes of pyruvate (>18 folds), UDPG (uridine diphosphate glucose), and aspartate as well as higher levels of secreted organic acids (e.g., malate and succinate). These results suggest that the ΔccmKLMN mutant is able to largely maintain a fluxome similar to the control strain by changing in intracellular metabolite concentrations and metabolite overflows under optimal growth conditions. When CO 2 was insufficient (0.2%), provision of acetate moderately promoted mutant growth. Interestingly, the removal of microcompartments may loosen the flux network and promote RuBisCO side-reactions, facilitating redirection of central metabolites to competing pathways (i.e., pyruvate to heterologous lactate production). This study provides important insights into metabolic regulation via enzyme compartmentation and cyanobacterial compensatory responses.

09 BIOMASS FUELS↗
DOE OSTI2019

Nanoparticle diffusion in sheared cellular blood flow

Using a multiscale blood flow solver, the complete diffusion tensor of nanoparticles (NPs) in sheared cellular blood flow is calculated over a wide range of shear rate and haematocrit. In the short-time regime, NPs exhibit anomalous dispersive behaviors under high shear and high haematocrit due to the transient elongation and alignment of the red blood cells (RBCs). In the long-time regime, the NP diffusion tensor features high anisotropy. Particularly, there exists a critical shear rate ( ${\sim}100~\text{s}^{-1}$ ) around which the shear-rate dependence of the diffusivity tensor changes from linear to nonlinear scale. Above the critical shear rate, the cross-stream diffusivity terms vary sublinearly with shear rate, while the longitudinal term varies superlinearly. The dependence on haematocrit is linear in general except at high shear rates, where a sublinear scale is found for the vorticity term and a quadratic scale for the longitudinal term. Through analysis of the suspension microstructure and numerical experiments, the nonlinear haemorheological dependence of the NP diffusion tensor is attributed to the streamwise elongation and cross-stream contraction of RBCs under high shear, quantified by a capillary number. The RBC size is shown to be the characteristic length scale affecting the RBC-enhanced shear-induced diffusion (RESID), while the NP submicrometre size exhibits negligible influence on the RESID. Based on the observed scaling behaviours, empirical correlations are proposed to bridge the NP diffusion tensor to specific shear rate and haematocrit. As a result, the characterized NP diffusion tensor provides a constitutive relation that can lead to more effective continuum models to tackle large-scale NP biotransport applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Robust Rapid Cellular Metabolite Sensing Using Benchtop NMR and SABRE-Hyperpolarized [1- 13 C]Pyruvate

Hyperpolarized NMR has emerged as a powerful analytical technique to significantly enhance targeted NMR signals, improving the sensitivity for investigations of unique chemical and biological dynamics. Here, we demonstrate the use of a hyperpolarization strategy based on Signal Amplification By Reversible Exchange (SABRE) to generate highly reproducible doses of a hyperpolarized [1- 13 C]pyruvate probe for benchtop characterization of yeast metabolism. This method allows rapid, scalable, and benchtop preparation of biocompatible hyperpolarized solutions suitable for live-cell experiments. We show that this production can be dove-tailed into a modular, compact workflow to characterize real-time metabolism in cell cultures, using Saccharomyces cerevisiae (Baker’s yeast) as a model organism. With high temporal resolution, we show that this method can resolve the conversion of hyperpolarized [1- 13 C]pyruvate into oxidative decarboxylation products CO 2 and bicarbonate. This conversion exhibits sustained and detectable metabolic activity for over 300 s after introduction of the agent to the cells. We model the metabolite kinetics to show decarboxylation activity and derive estimates of the pH over time from the CO 2 and bicarbonate (carbonic acid buffer system) equilibrium to probe changes in the cellular environment during active metabolism. These results highlight the utility of benchtop SABRE-hyperpolarized [1- 13 C]pyruvate as a scalable, specific probe for metabolic phenotyping of living cells using compact, low-cost instrumentation well-suited for future high-throughput applications across microbial engineering, drug response profiling, and dynamic metabolic screening.

fungi↗
DOE OSTI2024

A Cellular Automaton Simulation for Predicting Phase Evolution in Solid-State Reactions

New computational tools for solid-state synthesis recipe design are needed in order to accelerate the experimental realization of novel functional materials proposed by high-throughput materials discovery workflows. This work contributes a cellular automaton simulation framework for predicting the time-dependent evolution of intermediate and product phases during solid-state reactions as a function of precursor choice and amount, reaction atmosphere, and heating profile. The simulation captures the effects of reactant particle spatial distribution, particle melting, and reaction atmosphere. Reaction rates based on rudimentary kinetics are estimated using density functional theory data from the Materials Project and machine learning estimators for the melting point and the vibrational entropy component of the Gibbs free energy. The resulting simulation framework allows for the prediction of the likely outcome of a reaction recipe before any experiments are performed. We analyze five experimental solid-state recipes for BaTiO 3 , CaZrN 2 , and YMnO 3 found in the literature to illustrate the performance of the model in capturing reaction selectivity and reaction pathways as a function of temperature and precursor choice. This simulation framework offers an easier way to optimize existing recipes, aid in the identification of intermediates, and design effective recipes for yet unrealized inorganic solids in silico .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. In this work, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Biological Membrane Organization and Cellular Signaling

To execute their many vital functions, cell membranes are highly organized. Here, we review how membrane structure shapes signal transduction across membranes. Recent experimental and computational advances have shed significant light on mechanisms linking the function of membrane signaling proteins to the composition and physical properties of the membrane lateral structures in which they are embedded. We provide an overview of the structural characteristics of membranes containing heterogeneous mixtures of lipids and other molecules and summarize work on “raft” domains in model and cell membranes, as determined by microscopy, spectroscopy, neutron scattering, and computer simulations. We discuss the principles of partitioning of proteins into membranes and how the structure, dynamics, and function of membrane-embedded and peripheral proteins can be modulated by specific membrane components and physical properties of membranes and raft domains. Lastly, we report on challenges and future directions toward a molecular-level understanding of how membrane organization gives rise to various context-dependent cellular signaling.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Drizzle, Turbulence, and Density Currents Below Post Cold Frontal Open Cellular Marine Stratocumulus Clouds

Nine cases of postcold frontal marine stratocumulus clouds exhibiting open cellular mesoscale organization are analyzed to characterize the drizzle, turbulence, and density currents below them. Data collected by the vertically pointing Doppler cloud radar and multiple lidars part of the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic (ENA) site are used in these analyses. A total of 251 drizzle shafts passed over the site with 76 shafts sampled for more than 15 min by the vertically pointing instruments. On average the drizzle shafts were ~18 km wide with below-cloud drizzle water path of ~40 g m −2 , cloud base rain rate of 7.78 mm day −1 , and cloud base drizzle modal diameter of 393 μm. The widths of the drizzle shafts did not exhibit any relationship with the cloud base rain rate, below-cloud drizzle water path, and the total water removed from the cloud. The downdrafts in the lowest 500 m within the drizzle cells strengthened with increasing cloud base rain rates, while the updrafts within drizzle cells did not exhibit this behavior. On average, the surface air density, pressure, water vapor mixing ratio, and wind speed along the background wind during the drizzle shaft were higher by 1.88 g m −3 , 8.60 Pa, 0.24 g kg −1 , and 1.22 m s −1 , respectively, from their background values. On the other hand, the surface air temperature was lower by 0.43 K during the drizzle shaft than its background value. The coincident measurements highlight the drizzle-turbulence-surface coupling in these cloud systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mesoscale Cellular Convection Detection and Classification Using Convolutional Neural Networks: Insights From Long-Term Observations at ARM Eastern North Atlantic Site

Marine boundary layer clouds are crucial in Earth's climate system. They frequently manifest as closed or open cell mesoscale cellular convection (MCC). MCC clouds are challenging to represent accurately in current climate models, highlighting the need for detailed observational data sets and in-depth analyses. This study utilizes over 8 years of observations from the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) User Facility Eastern North Atlantic (ENA) site at Graciosa Island, Azores, to investigate these clouds. We first apply a convolutional neural network with a U-Net architecture to classify open and closed cells, marking the first application of such an approach for automatically detecting MCC patterns from ground-based radar measurements. This method addresses some observational gaps in satellite data related to low temporal resolution, nighttime challenges, and limited vertical structure capture. The analysis of the MCC cases shows clear differences between closed and open MCCs: Closed MCC clouds are characterized by lower cloud tops and bases, shallower cloud geometrical depth, weaker horizontal wind speeds, stronger atmospheric stability, and a more homogeneous liquid water path than open MCCs. Finally, we demonstrate two potential applications of our radar-based MCC classifications: (a) facilitating the investigation of aerosol-cloud interactions and (b) exploring meteorological factors along with MCC's evolution by integrating satellite imagery and back-trajectory analysis. The identified MCC cases offer a valuable resource for the scientific community to study MCC processes further and improve climate model accuracy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response

Protein arginine methyltransferases (PRMTs) regulate diverse biological processes and are increasingly being recognized for their potential as drug targets. Here we report the discovery of a potent, selective, and cell-active chemical probe for PRMT7. SGC3027 is a cell permeable prodrug, which in cells is converted to SGC8158, a potent, SAM-competitive PRMT7 inhibitor. Inhibition or knockout of cellular PRMT7 results in drastically reduced levels of arginine monomethylated HSP70 family stress-associated proteins. Structural and biochemical analyses reveal that PRMT7-driven in vitro methylation of HSP70 at R469 requires an ATP-bound, open conformation of HSP70. In cells, SGC3027 inhibits methylation of both constitutive and inducible forms of HSP70, and leads to decreased tolerance for perturbations of proteostasis including heat shock and proteasome inhibitors. These results demonstrate a role for PRMT7 and arginine methylation in stress response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle

Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nanoparticle cellular internalization is not required for RNA delivery to mature plant leaves

Rapidly growing interest in the nanoparticle-mediated delivery of DNA and RNA to plants requires a better understanding of how nanoparticles and their cargoes translocate in plant tissues and into plant cells. However, little is known about how the size and shape of nanoparticles influence transport in plants and the delivery efficiency of their cargoes, limiting the development of nanotechnology in plant systems. In this study we employed non-biolistically delivered DNA-modified gold nanoparticles (AuNPs) of various sizes (5-20 nm) and shapes (spheres and rods) to systematically investigate their transport following infiltration into Nicotiana benthamiana leaves. Generally, smaller AuNPs demonstrated more rapid, higher and longer-lasting levels of association with plant cell walls compared with larger AuNPs. We observed internalization of rod-shaped but not spherical AuNPs into plant cells, yet, surprisingly, 10 nm spherical AuNPs functionalized with small-interfering RNA (siRNA) were the most efficient at siRNA delivery and inducing gene silencing in mature plant leaves. These results indicate the importance of nanoparticle size in efficient biomolecule delivery and, counterintuitively, demonstrate that efficient cargo delivery is possible and potentially optimal in the absence of nanoparticle cellular internalization. Additionally, our results highlight nanoparticle features of importance for transport within plant tissues, providing a mechanistic overview of how nanoparticles can be designed to achieve efficacious biocargo delivery for future developments in plant nanobiotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) aims to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. Here, we present a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Neutral rhenium( i ) tricarbonyl complexes with sulfur-donor ligands: anti-proliferative activity and cellular localization

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anti-cancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO) 3 (SR)] complexes, where (NN) is 2,2'-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO) 3 (OH 2 )]+ complexes; however, one of the complexes, fac-[Re(CO) 3 (phen)(SC(Ph)CH 2 C(O)OMe)] (3b), was active (IC 50 ~ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac-[Re(CO) 3 (phen)(OH 2 )]+, this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO) 3 (SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λ ex = 405 nm, λ em = 470–570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗