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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Temporal Sampling of Enzymes from Live Cells by Localized Electroporation and Quantification of Activity by SAMDI Mass Spectrometry

Abstract Measuring changes in enzymatic activity over time from small numbers of cells remains a significant technical challenge. In this work, a method for sampling the cytoplasm of cells is introduced to extract enzymes and measure their activity at multiple time points. A microfluidic device, termed the live cell analysis device (LCAD), is designed, where cells are cultured in microwell arrays fabricated on polymer membranes containing nanochannels. Localized electroporation of the cells opens transient pores in the cell membrane at the interface with the nanochannels, enabling extraction of enzymes into nanoliter‐volume chambers. In the extraction chambers, the enzymes modify immobilized substrates, and their activity is quantified by self‐assembled monolayers for matrix‐assisted laser desorption/ionization (SAMDI) mass spectrometry. By employing the LCAD‐SAMDI platform, protein delivery into cells is demonstrated. Next, it is shown that enzymes can be extracted, and their activity measured without a loss in viability. Lastly, cells are sampled at multiple time points to study changes in phosphatase activity in response to oxidation by hydrogen peroxide. With this unique sampling device and label‐free assay format, the LCAD with SAMDI enables a powerful new method for monitoring the dynamics of cellular activity from small populations of cells.

Mukherjee, Prithvijit↗
NASA NTRS1998

Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber

A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell. Copyright 1998 Academic Press.

Non-NASA Center↗
DOE OSTI2025

A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells

The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.

SARS-CoV-2 main protease (Mpro/3CLpro)↗
NASA NTRS1997

Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells

Chromatin is thought to be structurally discontinuous because it is packaged into morphologically distinct chromosomes that appear physically isolated from one another in metaphase preparations used for cytogenetic studies. However, analysis of chromosome positioning and movement suggest that different chromosomes often behave as if they were physically connected in interphase as well as mitosis. To address this paradox directly, we used a microsurgical technique to physically remove nucleoplasm or chromosomes from living cells under isotonic conditions. Using this approach, we found that pulling a single nucleolus or chromosome out from interphase or mitotic cells resulted in sequential removal of the remaining nucleoli and chromosomes, interconnected by a continuous elastic thread. Enzymatic treatments of interphase nucleoplasm and chromosome chains held under tension revealed that mechanical continuity within the chromatin was mediated by elements sensitive to DNase or micrococcal nuclease, but not RNases, formamide at high temperature, or proteases. In contrast, mechanical coupling between mitotic chromosomes and the surrounding cytoplasm appeared to be mediated by gelsolin-sensitive microfilaments. Furthermore, when ion concentrations were raised and lowered, both the chromosomes and the interconnecting strands underwent multiple rounds of decondensation and recondensation. As a result of these dynamic structural alterations, the mitotic chains also became sensitive to disruption by restriction enzymes. Ion-induced chromosome decondensation could be blocked by treatment with DNA binding dyes, agents that reduce protein disulfide linkages within nuclear matrix, or an antibody directed against histones. Fully decondensed chromatin strands also could be induced to recondense into chromosomes with pre-existing size, shape, number, and position by adding anti-histone antibodies. Conversely, removal of histones by proteolysis or heparin treatment produced chromosome decondensation which could be reversed by addition of histone H1, but not histones H2b or H3. These data suggest that DNA, its associated protein scaffolds, and surrounding cytoskeletal networks function as a structurally-unified system. Mechanical coupling within the nucleoplasm may coordinate dynamic alterations in chromatin structure, guide chromosome movement, and ensure fidelity of mitosis.

NASA Discipline Cell Biology↗
NASA NTRS1972

Further observations on the phenomenon of secondary vacuolation in living cells.

The dynamics of secondary vacuole movement is studied in living hair cells of Tradescantia virginiana. The pattern of movement of these vacuoles is found to be similar to that described by the author previously for organelles in cultured cells. Evidence is presented in support of the thesis that the occurrence and dynamics of secondary vacuoles is a common phenomenon for plant cells.

Mahlberg, P.↗
DOE OSTI2021

Iron-Imprinted Single-Atomic Site Catalyst-Based Nanoprobe for Detection of Hydrogen Peroxide in Living Cells

Fe-based single-atomic site catalysts (SASCs), with the natural metalloproteases-like active site structure, have attracted widespread attention in biocatalysis and biosensing. Precisely, controlling the isolated single-atom Fe-N-C active site structure is crucial to improve the SASCs’ performance. In this work, we use a facile ion-imprinting method (IIM) to synthesize isolated Fe-N-C single-atomic site catalysts (IIM-Fe-SASC). With this method, the ion-imprinting process can precisely control ion at the atomic level and form numerous well-defined single-atomic Fe-N-C sites. The IIM-Fe-SASC shows better peroxidase-like activities than that of non-imprinted references. Due to its excellent properties, IIM-Fe-SASC is an ideal nanoprobe used in the colorimetric biosensing of hydrogen peroxide (H 2 O 2 ). Using IIM-Fe-SASC as the nanoprobe, in situ detection of H 2 O 2 generated from MDA-MB-231 cells has been successfully demonstrated with satisfactory sensitivity and specificity. This work opens a novel and easy route in designing advanced SASC and provides a sensitive tool for intracellular H 2 O 2 detection.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Manipulating cobalt oxide on N-doped aligned electrospun carbon nanofibers towards instant electrochemical detection of dopamine secreted by living cells

A demand exists for the development of miniaturized biosensors with high sensitivity and a wide dynamic range for rapid detecting dopamine (DA) levels. Here, an electrochemical sensor is created by decorating closely packed cobalt oxide (Co 3 O 4 ) nanograins on nitrogen-doped electrospun carbon nanofibers (NECNFs) via a facile electrodeposition method. The carbon nanofiber matrix provides both a scaffold with ultrahigh surface area for homogeneous dispersion of cobalt oxide nanostructures and facilitates the electrochemical conductivity for the hybrid electrode. The sensing principle is based on the redox reaction between DA and DA quinone that generates electrical signal, which is detectable via differential pulse voltammetry (DPV) and chronoamperometry (CA). Owing to a high electroactive surface area and facilitating electron transfer between electrode surface and the target molecule, the electrical sensing platform exhibits superior sensitivity and selectivity toward DA, with an excellent limit of detection (9 nM) over a wide range of concentrations (0.01 to 100 μM). Moreover, based on its excellent sensing properties and biocompatibility, the sensor has been used for the real-time monitoring exogeneous DA released from pheochromocytoma (PC12) cells. This work demonstrates promise of a novel sensor technology that may render rapid point-of-care testing of DA towards early clinical diagnosis.

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

Peptoid-Based Programmable 2D Nanomaterial Sensor for Selective and Sensitive Detection of H 2 S in Live Cells

During the past decades, a variety of two-dimensional (2D) nanosheets have been developed through supramolecular self-assembly. Among them, those assembled from sequence-defined molecules have received particularly attention because they enable a precise displaying of functional groups, including fluorescent dyes, within nanosheet surfaces. On the other hand, due to the fluorescence self-quenching, synthesis of organic 2D nanosheets exhibiting high fluorescence quantum yields is a significant challenge. Herein, we report the utilization of H 2 S-responsive probes as peptoid sidechains to design and synthesize crystalline 2D nanomembranes (2DNMs) as selective and sensitive H 2 S sensors. These 2DNM sensors exhibit a high quantum yield as a result of high crystallinity and tunable probe density. Compared with amorphous state of peptoid assembly and pre-assembled peptoid-probe conjugates, these crystalline 2DNM sensors exhibit a significantly strong fluorescence intensity and a high sensitivity (~ 0.36 nM). By sonication-cutting these 2DNM sensors into a colloidal form in aqueous solution, we further demonstrated the use of colloidal 2DNMs for detecting both exogenous and endogenous H 2 S inside cells or targeted cell organelles. As far as we know, this is the first example of using sequence-defined 2D nanomaterials for selective and sensitive detection of H 2 S. Because peptoids are biocompatible and peptoid-based 2DNMs are highly programmable, we expect that this new class of 2DNM sensors offer great potentials for detecting H 2 S and for biological applications.

2D nanomaterials↗
DOE OSTI2024

Live cell imaging of cellular dynamics in poplar wood using computational cannula microscopy

This study presents significant advancements in computational cannula microscopy for live imaging of cellular dynamics in poplar wood tissues. Leveraging machine-learning models such as pix2pix for image reconstruction, we achieved high-resolution imaging with a field of view of 55µm using a 50µm-core diameter probe. Our method allows for real-time image reconstruction at 0.29 s per frame with a mean absolute error of 0.07. We successfully captured cellular-level dynamics in vivo , demonstrating morphological changes at resolutions as small as 3µm. We implemented two types of probabilistic neural network models to quantify confidence levels in the reconstructed images. This approach facilitates context-aware, human-in-the-loop analysis, which is crucial for in vivo imaging where ground-truth data is unavailable. Using this approach we demonstrated deep in vivo computational imaging of living plant tissue with high confidence (disagreement score ⪅0.2). This work addresses the challenges of imaging live plant tissues, offering a practical and minimally invasive tool for plant biologists.

Ingold, Alexander (ORCID:0009000752380016)↗
DOE OSTI2024

Live-Cell Quantum Dot-Based Tracking of Plant & Microbial Extracellular Vesicles

All cellular organisms examined to date release various types of small vesicles called extracellular vesicles (EVs). They were originally thought to be unimportant, but research into EVs as carriers of key messages for communication within large, multicellular organisms or between interacting organisms has gained interest in many different scientific areas of study. Recently, it was discovered that both plants and their pathogenic fungi generate EVs and they are important vehicles for sending plant signals to thwart invasion by fungal pathogens, and in response, fungi use EVs to help evade plant defenses. This project aimed to develop new ways to visualize EVs and their potential nucleic acid cargo isolated from the crop plant, sorghum. We adapted a click chemistry-based method for making quantum dot-based RNA sensors, which will be a useful tool for others studying small RNAs. These sensors were not used detect RNA in sorghum EVs because unlike EVs from Arabidopsis, sorghum EVs were not enriched for specific small RNAs. This interesting difference shifted the project in an exciting direction, which focused on comparing EV proteomes. Our study discovered that greater than 60% of Arabidopsis EV proteins were also found in the sorghum EV proteome, revealing a partial conservation between a eudicot and monocot plant. These studies have raised new, fundamental questions on the conserved function of EVs in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

59 BASIC BIOLOGICAL SCIENCES↗