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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Fabrication of a novel 3D-printed perfusion bioreactor for complex cell culture models

We introduce a novel fabrication method for developing a 3D-printed perfusion bioreactor (3D-PBR) to facilitate the in situ growth and differentiation of human bone marrow (BM)-derived mesenchymal stem cells (MSCs) while enabling coculture with vascular cells. To recapitulate human physiology, in vitro platforms must incorporate several key features of their native target organ. This often entails a supportive 3D architecture for growing and differentiating multiple human cell types in situ under perfusion. Other essential characteristics include reproducibility, ease of customization, and biocompatibility. Our 3D-PBR combines these features and was fabricated using a biocompatible resin-based polymer, which was 3D-printed, followed by the addition of a permeable membrane to create a coculture microenvironment. MSCs were encapsulated in a collagen-fibrin gel alongside human endothelium within the 3D-PBR. The physical cues that our 3D-PBR provided facilitated the differentiation of MSCs into specific lineages, such as adipocytes and osteoblasts. Immunohistochemistry images demonstrated that cells grown in the 3D-PBR exhibited more physiologically relevant BM perivascular niche markers compared to static culture models. Our method utilizes emerging 3D printing techniques and alternative materials, departing from traditional PDMS-based soft lithography. These advancements in fabrication further enhance in vitro platforms for diverse cell culture models and vascular permeability assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls

Many insects have evolved the ability to manipulate plant growth to generate extraordinary structures called galls, in which insect larva can develop while being sheltered and feeding on the plant. In particular, cynipid (Hymenoptera: Cynipidae) wasps have evolved to form morphologically complex galls and generate an astonishing array of gall shapes, colors, and sizes. However, the biochemical basis underlying these remarkable cellular and developmental transformations remains poorly understood. A key determinant in plant cellular development is cell wall deposition that dictates the physical form and physiological function of newly developing cells, tissues, and organs. However, it is unclear to what degree cell walls are restructured to initiate and support the formation of new gall tissue. Here, we characterize the molecular alterations underlying gall development using a combination of metabolomic, histological, and biochemical techniques to elucidate how valley oak (Quercus lobata) leaf cells are reprogrammed to form galls. Strikingly, gall development involves an exceptionally coordinated spatial deposition of lignin and xylan to form de novo gall vasculature. Our results highlight how cynipid wasps can radically change the metabolite profile and restructure the cell wall to enable the formation of galls, providing insights into the mechanism of gall induction and the extent to which plants can be entirely reprogrammed to form unique structures and organs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Lack of xyloglucan in the cell walls of the Arabidopsis xxt1/xxt2 mutant results in specific increases in homogalacturonan and glucomannan

Mutations in both ArabidopsisXyloglucan Xylosyltransferase1 (XXT1) and Xyloglucan Xylosyltransferase2 (XXT2) result in the absence of the major hemicellulose, xyloglucan (XyG). The growth physiology, tensile strength, and cell wall compositions of etiolated hypocotyls of xxt1/xxt2 double and xxt1/xxt2/xxt5 triple mutants were characterized and compared with those of mur2 and mur3 mutations that alter the side group composition of XyG. Wild type and mur2 demonstrated normal elongation growth, whereas the xxt double and triple mutants and mur3 showed reduced elongation and cell swelling at the base of the hypocotyl at the later stages of elongation. Whereas mur3 hypocotyls had reduced tensile strength, the xxt double and triple mutants had similar tensile strengths as wild type, but reached breaking points at lower strains. Loss of XyG in hypocotyls and rosette leaf cell walls was associated with specific increases in the relative abundance of homogalacturonan and the hemicellulose glucomannan, but not arabinoxylan. The increased homogalacturonan and glucomannan abundance did not result from enhanced expression of their polymer synthases. An analysis of published transcriptomic data indicated that genes encoding some members of the expansin, xyloglucan endotransglucosylase/hydrolase, arabinogalactan-protein, and structural protein families were upregulated in the xxt mutants. We hypothesize that an as yet unknown mechanism exists by which pectin and hemicellulose abundance can be altered other than by increased rates of biosynthesis to maintain a structurally sound cell wall.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence

Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Fluorescence-coupled micropipette aspiration assay to examine calcium mobilization caused by red blood cell mechanosensing

Abstract Mechanical stimuli such as tension, compression, and shear stress play critical roles in the physiological functions of red blood cells (RBCs) and their homeostasis, ATP release, and rheological properties. Intracellular calcium (Ca 2+ ) mobilization reflects RBC mechanosensing as they transverse the complex vasculature. Emerging studies have demonstrated the presence of mechanosensitive Ca 2+ permeable ion channels and their function has been implicated in the regulation of RBC volume and deformability. However, how these mechanoreceptors trigger Ca 2+ influx and subsequent cellular responses are still unclear. Here, we introduce a fluorescence-coupled micropipette aspiration assay to examine RBC mechanosensing at the single-cell level. To achieve a wide range of cell aspirations, we implemented and compared two negative pressure adjusting apparatuses: a homemade water manometer (− 2.94 to 0 mmH 2 O) and a pneumatic high-speed pressure clamp (− 25 to 0 mmHg). To visualize Ca 2+ influx, RBCs were pre-loaded with an intensiometric probe Cal-520 AM, then imaged under a confocal microscope with concurrent bright-field and fluorescent imaging at acquisition rates of 10 frames per second. Remarkably, we observed the related changes in intracellular Ca 2+ levels immediately after aspirating individual RBCs in a pressure-dependent manner. The RBC aspirated by the water manometer only displayed 1.1-fold increase in fluorescence intensity, whereas the RBC aspirated by the pneumatic clamp showed up to threefold increase. These results demonstrated the water manometer as a gentle tool for cell manipulation with minimal pre-activation, while the high-speed pneumatic clamp as a much stronger pressure actuator to examine cell mechanosensing directly. Together, this multimodal platform enables us to precisely control aspiration and membrane tension, and subsequently correlate this with intracellular calcium concentration dynamics in a robust and reproducible manner.

Wang, Haoqing↗
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 OSTI2020

Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma

Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape and characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome. Hypo-methylated regions are enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated regions are enriched in polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered methylation in promoters, enhancers, and gene bodies, as well as in polycomb repressive complex occupancy and CTCF binding sites are associated with cancer-specific gene dysregulation. Epigenetic-mediated activation of non-canonical WNT/β-catenin/MMP signaling and a YY1/lncRNA ESCCAL-1/ribosomal protein network are uncovered and validated as potential novel ESCC driver alterations. This study advances our understanding of how epigenetic landscapes shape cancer pathogenesis and provides a resource for biomarker and target discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Characterization of cellular oxidative stress response by stoichiometric redox proteomics

The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function, including activity, binding, conformation, localization, and interactions with other molecules. It is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs in order to elucidate the complex redox landscape and identify novel redox regulators in signaling and regulation. Mass spectrometry-based redox proteomics has emerged as the primary platform for enabling the broad characterization of thiol PTMs in cells and tissues. Herein we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs in cells and tissues at physiological or oxidative stress conditions and highlight some recent applications using these enabling techniques. Considering the relative maturity of available methods, a primary emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives towards a better understanding of cellular redox regulatory networks in cells and tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fluorescent toxins as ion channel activity sensors.

Voltage gated ion channels (VGICs) shape the electrical character of cells by undergoing structural changes in response to membrane depolarization. High-resolution techniques have provided a wealth of data on individual VGIC structures, but the conformational changes of endogenous channels in live cell membranes have remained unexplored. Here, we describe methods for imaging structural changes of voltage-gated K + channels in living cells, using peptidyl toxins labeled with fluorophores that report specific protein conformations. These Endogenous Voltage-sensor Activity Probes (EVAPs) enable study of both VGIC allostery and function in the context of endogenous live-cell membranes under different physiological states. In this chapter, we describe methods for the synthesis, imaging, and analysis of dynamic EVAPs, which can report K + channel activity in complex tissue preparations via 2-photon excitation microscopy, and environment-sensitive EVAPs, which report voltage-dependent conformational changes at the VGIC-toxin interface. The methods here present the utility of current EVAPs and lay the groundwork for the development of other probes that act by similar mechanisms. EVAPs can be correlated with electrophysiology, offering insight into the molecular details of endogenous channel function and allostery in live cells. This enables investigation of conformational changes of channels in their native, functional states, putting structures and models into a context of live-cell membranes. The expansive array of state-dependent ligands and optical probes should enable probes more generally for investigating the molecular motions of endogenous proteins.

Stewart, Robert↗
DOE OSTI2020

A grass-specific cellulose–xylan interaction dominates in sorghum secondary cell walls

Abstract Sorghum ( Sorghum bicolor L. Moench) is a promising source of lignocellulosic biomass for the production of renewable fuels and chemicals, as well as for forage. Understanding secondary cell wall architecture is key to understanding recalcitrance i.e. identifying features which prevent the efficient conversion of complex biomass to simple carbon units. Here, we use multi-dimensional magic angle spinning solid-state NMR to characterize the sorghum secondary cell wall. We show that xylan is mainly in a three-fold screw conformation due to dense arabinosyl substitutions, with close proximity to cellulose. We also show that sorghum secondary cell walls present a high ratio of amorphous to crystalline cellulose as compared to dicots. We propose a model of sorghum cell wall architecture which is dominated by interactions between three-fold screw xylan and amorphous cellulose. This work will aid the design of low-recalcitrance biomass crops, a requirement for a sustainable bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Converting methoxy groups on lignin-derived aromatics from a toxic hurdle to a useful resource: a systems-driven approach

Lignin conversion to bioproducts is challenging for several reasons, including the toxicity generated from the abundant methoxy groups released as formaldehyde. Consequently, our project used the best understood methylotroph – for which there is growing knowledge of formaldehyde stress responses – to explore how genetic factors and single-cell phenotypic heterogeneity contribute to growth and production. Our major goals were to (1) understand the fundamentals of Methylobacterium growth on aromatics, (2) identify and understand the basis of physiological basis of single-cell heterogeneity, and (3) develop quantitative models that relate heterogeneity to physiological and evolutionary outcomes.

Source record↗
DOE OSTI2020

Skeletal tissue regulation by catalase overexpression in mitochondria

Accumulation of oxidative damage from excess reactive oxygen species (ROS) may contribute to skeletal aging and mediate adverse responses to physiological challenges. Wild-type (WT) mice and transgenic mice (male, 16 wk of age) with human catalase targeted to the mitochondria (mCAT) were analyzed for skeletal responses to the remodeling stimuli of combined hind-limb unloading and exposure to ionizing radiation ( 137 Cs, 2 Gy). Treatment for 2 wk caused lipid peroxidation in the bones WT but not mCAT mice, showing that transgene expression mitigated oxidative stress. Ex vivo osteoblast colony growth rate was 95% greater in mCAT than WT mice and correlated with catalase activity levels ( P < 0.005, r = 0.67), although terminal osteoblast and osteoclast differentiation were unaffected. mCAT mice had lower cancellous bone volume and cortical size than WT mice. Ambulatory control mCAT animals also displayed reduced cancellous and cortical structural properties compared with control WT mice. In mCAT but not WT mice, treatment caused an unexpectedly rapid radial expansion (+8% cortical area, +22% moment of inertia), reminiscent of compensatory bone growth during advancing age. In contrast, treatment caused similar structural deficits in cancellous tissue of mCAT and WT mice. In sum, mitochondrial ROS signaling via H 2 O 2 was important for the acquisition of adult bone structure and catalase overexpression failed to protect cancellous tissue from treatment. In contrast, catabolic stimuli caused radial expansion in mCAT not WT mice, suggesting that mitochondrial ROS in skeletal cells act to suppress tissue turnover in response to remodeling challenges.

Cell Biology↗
DOE OSTI2025

Machine learning models for segmentation and classification of cyanobacterial cells

Abstract Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells. Here, we describe a newly developed software package called Cypose which uses machine learning (ML) models to solve two specific tasks: segmentation of individual cyanobacterial cells, and classification of cellular phenotypes. The segmentation models are based on the Cellpose framework, while classification is performed using a convolutional neural network named Cyclass. To our knowledge, these are the first developed ML-based models for cyanobacteria segmentation and classification. When compared to other methods, our segmentation models showed improved performance and were able to segment cells with varied morphological phenotypes, as well as differentiate between live and lysed cells. We also found that our models were robust to imaging artifacts, such as dust and cell debris. Additionally, the classification model was able to identify different cellular phenotypes using only images as input. Together, these models improve cell segmentation accuracy and enable high-throughput analysis of dense cyanobacterial colonies and filamentous cyanobacteria.

Huffine, Clair A.↗
DOE OSTI2024

Unraveling the Combined Photothermal Stability of Common Perovskite Solar Cell Compositions

In halide perovskite solar cells, certain compositions, especially those with a high mixture of anions, degrade rapidly. Here, in this study, a degradation study compares the photo (exposure to light), thermal (exposure to elevated temperatures), and photo-plus-thermal (combination) stability of three representative perovskite compositions chosen for their relatively high performance and to independently test anion versus cation effects. Based upon experience and reports, the compositions studied are triple cation with a high Br ratio (Cs 0.05 (FA 0.98 MA 0.02 ) 0.95 Pb(I 0.5 Br 0.5 ) 3 ), all iodide with a moderately high Cs ratio (FA 0.8 Cs 0.2 PbI 3 ), and FA-dominated triple cation (Cs 0.05 (FA 0.98 MA 0.02 ) 0.95 Pb(I 0.98 Br 0.02 ) 3 ). Cs 0.05 (FA 0.98 MA 0.02 ) 0.95 Pb(I 0.98 Br 0.02 ) 3 displayed the best combined photo-plus-thermal stability. Degradation mechanisms were investigated by comparing the morphology, surface composition, and bulk and interface carrier dynamics. Under the harshest aging conditions (photo-plus-thermal), phase segregation and vaporization of organic cations occurred, along with the appearance of high-energy states indicating the interaction with C 60 . The findings were verified on perovskite films blade-coated in air used in devices (FTO/NiOx/SAM/Perovskite/C 60 /BCP/Cu), achieving an efficiency of 21.9% alongside correlated stability.

14 SOLAR ENERGY↗
DOE OSTI2023

Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase

The function of cellobiose dehydrogenase (CDH) in biosensors, biofuel cells, and as a physiological redox partner of lytic polysaccharide monooxygenase (LPMO) is based on its role as an electron donor. Before donating electrons to LPMO or electrodes, an interdomain electron transfer from the catalytic FAD-containing dehydrogenase domain to the electron shuttling cytochrome domain of CDH is required. This study investigates the role of two crucial amino acids located at the dehydrogenase domain on domain interaction and interdomain electron transfer by structure-based engineering. The electron transfer kinetics of wild-type Myriococcum thermophilum CDH and its variants M309A, R698S, and M309A/R698S were analyzed by stopped-flow spectrophotometry and structural effects were studied by small-angle X-ray scattering. The data show that R698 is essential to pull the cytochrome domain close to the dehydrogenase domain and orient the heme propionate group towards the FAD, while M309 is an integral part of the electron transfer pathway – its mutation reducing the interdomain electron transfer 10-fold. Structural models and molecular dynamics simulations pinpoint the action of these two residues on the domain interaction and interdomain electron transfer.

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

ER stress and viral defense: Advances and future perspectives on plant unfolded protein response in pathogenesis

Viral infections pose significant threats to crop productivity and agricultural sustainability. The frequency and severity of these infections are increasing, and pathogens are evolving rapidly under the influence of climate change. This underscores the importance of exploring the fundamental mechanisms by which plants defend themselves against dynamic viral threats. One such mechanism is the unfolded protein response (UPR), which is activated when the protein folding demand exceeds the capacity of the endoplasmic reticulum, particularly under adverse environmental conditions. While the key regulators of the UPR in response to viral infections have been identified, our understanding of how they modulate the UPR to suppress plant viral infections at the molecular and genetic levels is still in its infancy. Recent findings have shown that, in response to plant viral infections, the UPR swiftly reprograms transcriptional changes to support cellular, metabolic, and physiological processes associated with cell viability. However, the underlying mechanisms and functional outcomes of these changes remain largely unexplored. Here, we highlight recent advances in plant UPR research and summarize key findings related to viral infection–induced UPR, focusing on the balance between prosurvival and prodeath strategies. We also discuss the potential of systems-level approaches to uncover the full extent of the functional link between the UPR and plant responses to viral infections.

ER stress↗