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All sources NASA NTRS DOE OSTI

DOE OSTI2024

Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Effect of Formation Heterogeneity on CO 2 Dissolution in Subsurface Porous Media

Dissolution trapping is one of the most dominant mechanisms for the secure storage of CO 2 injected in porous subsurface formations saturated with brine. This trapping mechanism is enhanced by convective mixing, which occurs due to the gravitational instability between the different fluid layers in the aquifer. The reservoir permeability also plays a crucial role in the dissolution rate and overall fluid flow dynamics during the density-driven convection in porous media. Herein this study investigates the role of complex heterogeneity, i.e., irregular permeability distribution in CO 2 dissolution, using a novel experimental approach to create medium permeability heterogeneity in Hele–Shaw cells. Complex subsurface transport phenomena such as a preferential dissolution path, CO 2 sweep efficiency, changes in finger morphology, and CO 2 concentration distribution are visualized by creating heterogeneous media. Experimental results showed that reservoir permeability heterogeneity causes significant channeling effects and poor sweep efficiency. A scaling relationship between average finger growth rate (Gr) and permeability (k) was obtained as Gr [m s –1 ] = 266.8k [m 2 ] + 1.20 × 10 –6 . Furthermore, the mass of CO 2 dissolved is calculated using the spectrophotometric method to characterize the convective instability. The convective flux was analyzed by comparing the experimental dissolution flux with the theoretical diffusion flux, calculating a maximum Sherwood number of 6.8. The study’s findings improve the current understanding of the CO 2 convection morphology in heterogeneous media, allowing better assessment of long-term CO 2 storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Longitudinal Single‐Cell Imaging of Engineered Strains with Stimulated Raman Scattering to Characterize Heterogeneity in Fatty Acid Production

Abstract Understanding metabolic heterogeneity is critical for optimizing microbial production of valuable chemicals, but requires tools that can quantify metabolites at the single‐cell level over time. Here, longitudinal hyperspectral stimulated Raman scattering (SRS) chemical imaging is developed to directly visualize free fatty acids in engineered Escherichia coli over many cell cycles. Compositional analysis is also developed to estimate the chain length and unsaturation of the fatty acids in living cells. This method reveals substantial heterogeneity in fatty acid production among and within colonies that emerges over the course of many generations. Interestingly, the strains display distinct types of production heterogeneity in an enzyme‐dependent manner. By pairing time‐lapse and SRS imaging, the relationship between growth and production at the single‐cell level are examined. The results demonstrate that cell‐to‐cell production heterogeneity is pervasive and provides a means to link single‐cell and population‐level production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer’s patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.

Life Sciences & Biomedicine - Other Topics↗

NASA NTRSDate not supplied

Graphical User Interface (GUI) Implementation for Agent-Based Microbial Radiobiology Model

Sending human life past the Low Earth Orbit (LEO) to explore the Moon and Mars will be challenging. The Earth’s magnetic field naturally protects life from deep-space particle radiation such as Galactic Cosmic Rays (GCR) and Solar Particle Events (SPE); these will pose health risks to humans in deep space. Research has been done to investigate these effects, like BioSentinel, the first biological CubeSat to fly beyond the LEO, designed to culture yeast in a microfluidic device and record optical measurements of growth and metabolism. However, experiments can only report cell damage as bulk growth curves, while deep-space radiation causes damage that is heterogeneous among individual cells. AMMPER is an open-source, agent-based, computational model coded in Python to simulate the effects of deep-space radiation on individual yeast cells (Saccharomyces cerevisiae) to facilitate interpretation of biological radiation experiments. Version 1.0 of the code ran in a command line interface (CLI), limiting use to those familiar with modularization, object-oriented programming, and computational models. Here we present a graphical user interface (GUI) for AMMPER to increase its accessibility. GUI development included converting input points and UI files, designing an application and logo, and expanding program packages. Additionally, we added optical assistance that corresponded with simulation parameters, which included simulation type, cell type, ROS model, and radiation dosage, as well as customizable display and file exportation features. Following a pilot testing period, its structure was updated further to enhance abilities, adding increased runs, video visualization, data plotting, and an educational/tutorial component. Future work will include creating a bit installer and runtime environment for AMMPER. Ultimately, the creation of the GUI has two main goals: to facilitate the integration of computational models into the work of researchers in microbial radiobiology, and to act as an interactive and visual resource for space biology education.

yeast↗

DOE OSTI2022

Impact of battery cell imbalance on electric vehicle range

Due to manufacturing variation, battery cells often possess heterogeneous characteristics, leading to battery state-of-charge variation in real-time. Since the lowest cell state-of-charge determines the useful life of battery pack, such variation can negatively impact the battery performance and electric vehicles range. Existing research has been focused on control design to mitigate cell imbalance. However, it is yet unclear how much impacts the cell imbalance can have on electric vehicle range. This paper closes this knowledge gap by using a simulation environment consisting of real-world driving speed data, vehicle longitudinal control, propulsion and vehicle dynamics, and cell level battery modeling. In particular, each battery cell is modeled as an equivalent circuit model, and variations among cell parameters are introduced to assess their impact on electric vehicles range and to identify the most influential parameter variations. Simulation results and analysis can be used to assist balancing control design and to benchmark control performance.

25 ENERGY STORAGE↗

DOE OSTI2021

Novel theranostic agent for PET imaging and targeted radiopharmaceutical therapy of tumour-infiltrating immune cells in glioma

Background: Malignant gliomas are deadly tumours with few therapeutic options. Although immunotherapy may be a promising therapeutic strategy for treating gliomas, a significant barrier is the CD11b + tumour-associated myeloid cells (TAMCs), a heterogeneous glioma infiltrate comprising up to 40% of a glioma's cellular mass that inhibits anti-tumour T-cell function and promotes tumour progression. A theranostic approach uses a single molecule for targeted radiopharmaceutical therapy (TRT) and diagnostic imaging; however, there are few reports of theranostics targeting the tumour microenvironment. Methods: Utilizing a newly developed bifunctional chelator, Lumi804, an anti-CD11b antibody (αCD11b) was readily labelled with either Zr-89 or Lu-177, yielding functional radiolabelled conjugates for PET, SPECT, and TRT. Findings: 89 Zr/ 177 Lu-labeled Lumi804-αCD11b enabled non-invasive imaging of TAMCs in murine gliomas. Additionally, 177 Lu-Lumi804-αCD11b treatment reduced TAMC populations in the spleen and tumour and improved the efficacy of checkpoint immunotherapy. Interpretation: 89 Zr- and 177 Lu-labeled Lumi804-αCD11b may be a promising theranostic pair for monitoring and reducing TAMCs in gliomas to improve immunotherapy responses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Mixing Matters: Nanoscale Heterogeneity and Stability in Metal Halide Perovskite Solar Cells

The structural stability of the metal halide perovskite (MHP) absorber material is crucial for the long-term solar cell stability in this thin-film photovoltaic technology. Here, we use mixed A-site FA0.83Cs0.17PbI3 to demonstrate that nanoscale compositional heterogeneity can serve as initiation sites for more macroscale, irreversible phase segregation, which causes device performance degradation. Probing compositional heterogeneity on length scales that has not been detected with conventional characterization techniques, we analyze the tetragonal to cubic phase transition behavior to indirectly determine the level of nanoscale compositional heterogeneity in the initial films. Further, we show that the thermal annealing conditions of the MHP layer during film processing influence the initial nanoscale compositional heterogeneity, and changing these processing conditions can be used to improve the device performance stability. The insights into structural degradation mechanisms initiated by nanoscale compositional heterogeneity and the proposed mitigation strategies will help guide the way toward long-term stable MHP solar cells.

14 SOLAR ENERGY↗

NASA NTRS1982

A parameterized model for the evolution of isotopic heterogeneities in a convecting system

It is experimentally shown that, although steady convective flows are efficient means to heterogeneity within a single cell, they do not produce a dispersal of heterogeneous material over scales that are large by comparison to their depth, which requires that the flow be time-dependent on a time scale comparable to the overturn time. Convection in an internally heated layer does possess this property, and numerical solutions are presently used to study the way in which it disperses a set of neutrally bouyant particles initially confined to a small space. The derived concept of effective diffusivity is applied to the isotopic evolution of the Sm-Nd and Rb-Sr systems, with spatial variations generated by horizontal variations in degree of melting 1.8 billion years ago.

Richter, F. M.↗

DOE OSTI2023

The use of synchrotron X-ray fluorescent imaging to study distribution and content of elements in chemically fixed single cells: a case study using mouse pancreatic beta-cells

Synchrotron X-ray fluorescence microscopy (SXRF) presents a valuable opportunity to study the metallome of single cells because it simultaneously provides high-resolution subcellular distribution and quantitative cellular content of multiple elements. Different sample preparation techniques have been used to preserve cells for observations with SXRF, with a goal to maintain fidelity of the cellular metallome. In this case study, mouse pancreatic beta-cells have been preserved with optimized chemical fixation. We show that cell-to-cell variability is normal in the metallome of beta-cells due to heterogeneity and should be considered when interpreting SXRF data. Additionally, we determined the impact of several immunofluorescence (IF) protocols on metal distribution and quantification in chemically fixed beta-cells and found that the metallome of beta-cells was not well preserved for quantitative analysis. However, zinc and iron qualitative analysis could be performed after IF with certain limitations. To help minimize metal loss using samples that require IF, we describe a novel IF protocol that can be used with chemically fixed cells after the completion of SXRF.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Advances in Cell Wall Matrix Research with a Focus on Mixed-Linkage Glucan

Mixed β(1,3;1,4)-linkage glucan (MLG) is commonly found in the monocot lineage, at particularly high levels in the Poaceae family, but also in the evolutionally distant genus, Equisetum. MLG has several properties that make it unique from other plant cell wall polysaccharides. It consists of β1,4-linked polymers of glucose interspersed with β1,3-linkages, but the presence of β1,3-linkages provides quite different physical properties compared to its closest form of the cell wall component, cellulose. The mechanisms of MLG biosynthesis have been investigated to understand whether single or multiple enzymes are required to build mixed linkages in the glucan chain. Currently, MLG synthesis by a single enzyme is supported by mutagenesis analyses of cellulose synthase-like F6, the major MLG synthase, but further investigation is needed to gather mechanistic insights. Because of transient accumulation of MLG in elongating cells and vegetative tissues, several hypotheses have been proposed to explain the role of MLG in the plant cell wall. Studies have been carried out to identify gene expression regulators during development and light cycles as well as enzymes involved in MLG organization in the cell wall. A role of MLG as a storage molecule in grains is evident, but the role of MLG in vegetative tissues is still not well understood. Characterization of a cell wall component is difficult due to the complex heterogeneity of the plant cell wall. Furthermore, as detailed in this review, recent exciting research has made significant impacts in the understanding of MLG biology in plants.

Transglucosylase/hydrolase (XTH)↗

NASA NTRS1990

Modelling a nickel-cadmium battery as a heterogeneous device

A common failure mode for nickel-cadmium batteries involves a nonuniform degradation of the performance of individual cells. This behavior is manifested as a divergence in voltage during cyclic operation. An empirically based performance model is presented which simulates a battery composed of heterogeneous cells. Battery performance is studied as a function of the distribution of cell performance characteristics. The technique has successfully predicted cell voltage divergence behavior observed during cycle life testing. It is noted that this work enhances understanding of life-test results and may improve life-test design and data analysis.

Glueck, Peter R.↗

NASA NTRS1987

Morphometrics of cellular damage in mice testis receiving X-ray and high-energy particle irradiation

Murine tests were exposed to single, low doses of either X-ray, helium, or argon radiation. Animals were sacrificed seventy-two hours later. Testes were fixed for transmission electron microscopy (TEM) and sectioned at either 60 nm for TEM observation or at 2 micron for counting using routine light microscope methods. Counts of the total population of surviving spermatogonia, including all type A cells, intermediate, and type B cells, were taken from tubule cross sections identified as Stage 6 and Stage 1 according to spermatogonial configuration. The surviving fraction of spermatogonia as compared to control, S/S sub o, was calculated for each dose. For both ions and X-rays, there was a rapid decline in survival at dose levels of .10 to .15 Gy in Stage 6 tubules. This was followed by a more gradual decrease in population. At higher doses, 0.30 Gy for argon and 0.80 Gy for helium and X-rays, the cell survival rates declined rapidly. Pre-leptotene spermatocytes in Stage 1 tubules exhibited a different survival curve indicating the extreme radio-sensitivity of type B spermatogonia. Data verify that the seminiferous tubules are composed of a heterogeneous population of cells with different radio-sensitivities and that these differences are manifested even at very low doses.

Sapp, Walter J.↗

DOE OSTI2026

Multimodal Nanoscale Mapping of Local Structure and CO 2 Adsorption in Metal–Organic Frameworks

Diamine functionalization of the metal−organic framework Mg 2 (dobpdc) (dobpdc 4− = 4,4′-dioxidobiphenyl-3,3′-dicarboxylate) significantly enhances its selectivity for CO 2 capture from flue gases and air. The structure and CO 2 capacity of such materials are typically assessed using bulk techniques that rely on averaging signal over large ensembles of unit cells, obscuring local heterogeneities, such as variations in CO 2 occupancy across individual nanocrystals. To resolve this limitation, we demonstrate a multimodal, nanoscale characterization of Mg 2 (dobpdc) appended with 1,3-diaminopropane. By employing recently developed characterization techniques at progressively smaller length scales, we uncover insights from correspondingly smaller populations of unit cells. First, we use parallel-beam 3D electron diffraction (3D ED) to identify a prominent expansion in lattice parameters upon desorption of CO 2 , as observed at the level of single nanocrystals. Second, we use convergent-probe 4D scanning transmission electron microscopy (4D-STEM) to quantify associated differences in lattice strain as a function of gas loading and diamine appending. These measurements sample small subvolumes within individual nanocrystals. Finally, we apply infrared scattering scanning near-field optical microscopy (IR s- SNOM) to confirm variable CO 2 chemisorption across adsorption sites at the surface of single nanocrystals. This multimodal, multiscale approach allows us to map heterogeneity within individual nanocrystals. Collectively, these findings emphasize the importance of local, nanoscale characterization of metal−organic frameworks in revealing previously unresolvable features that impact their performance.

Karstens, Sarah L. [University of California, Berk↗

DOE OSTI2023

A fast Fourier transform-based solver for elastic micropolar composites

This work presents a spectral micromechanical formulation for obtaining the full-field and homogenized response of elastic micropolar composites. The algorithm relies on a coupled set of convolution integral equations for the micropolar strains, where periodic Green’s operators associated with a linear homogeneous reference medium are convolved with functions of the Cauchy and couple stress fields that encode the material’s heterogeneity, as well as any potential material nonlinearity. Such convolution integral equations take an algebraic form in the reciprocal Fourier space that can be solved iteratively. In this vein, the fast Fourier transform (FFT) algorithm is leveraged to accelerate the numerical solution, resulting in a mesh-free formulation in which the periodic unit cell representing the heterogeneous material can be discretized by a regular grid of pixels in two dimensions (or voxels in three dimensions). For verification, the numerical solutions obtained with the micropolar FFT solver are compared with analytical solutions for a matrix with a dilute circular inclusion subjected to plane strain loading. The developed computational framework is then used to study length-scale effects and effective (micropolar) moduli of composites with various topological configurations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Physics-Based Model to Represent Membrane-Electrode Assemblies of Solid-Oxide Fuel Cells Based on Gadolinium-Doped Ceria

This paper reports a physics-based model that predicts membrane-electrode assembly (MEA) performance of solid-oxide fuel cells (SOFCs) with Ce 0.9 Gd 0.1 O 2− δ (GDC10) electrolyte membranes. The paper derives self-consistent thermodynamic and transport properties for GDC1o mobile charged defects (oxide vacancies and reduced-ceria small polarons) by fitting published measurements of oxygen non-stoichiometry and conductivity over ranges of temperature and O 2 partial pressures. The button-cell model is applied to evaluate how mixed ionic-electronic conductivity influences the performance of an SOFC MEA with a GDC10 electrolyte sandwiched between a porous, composite Ni-GDC10 anode and a porous, composite cathode of Sm 0.5 Sr 0.5 CoO 3− δ (i.e., SSC) and GDC10. SSC properties are also derived by fitting published conductivity and oxygen non-stoichiometry measurements. Mixed conductivity of GDC10 and competing charge transfer reactions at both electrodes reduce open circuit voltages due to leakage current and buildup of defect concentrations at electrode-electrolyte interfaces. To fit polarization data, the button-cell model includes heterogeneous reaction rates for defect incorporation on the GDC10 surface along with Butler–Volmer expressions derived for competing charge transfer reaction rates from rigorous analyses assuming rate-limiting, elementary charge transfer reactions for each electrode. The calibrated MEA model can support rigorous SOFC modeling with GDC10 electrolytes over the range of conditions within a fully operating cell.

Electrochemistry↗

DOE OSTI2023

Response of ZrC to swift heavy ion irradiation

Zirconium carbide (ZrC) is commonly used for energy sector research, as well as a surrogate for the proposed advanced nuclear fuel candidate uranium carbide. Here this study investigates structural modifications to nanocrystalline and microcrystalline ZrC resulting from dense electronic excitations induced by swift heavy ion exposure. Samples were irradiated with 946 MeV Au ions to various fluences up to 6 × 10 13 ions cm –2 and characterized using synchrotron-based x-ray diffraction. The evolution of the unit-cell parameter and heterogeneous microstrain were evaluated as a function of fluence and compared with those of nanocrystalline and microcrystalline CeO 2 (a surrogate for UO 2 fuel) irradiated under identical conditions. Distinct differences were observed in the radiation responses of the carbide and oxide across both grain sizes. Most notably, microcrystalline ZrC exhibits swelling characterized by two distinct regimes, which does not result in saturation at the ion fluences achieved. This contrasts with CeO 2 , which exhibits the well-documented direct-impact defect accumulation mechanism, reaching a steady-state saturation of swelling at higher fluences. Nanocrystalline CeO 2 undergoes more pronounced swelling compared with microcrystalline CeO 2 , in contrast to nanocrystalline ZrC, which exhibits only minimal unit-cell changes. These results demonstrate that swift heavy ion-induced structural changes can be quite different in carbides and oxides, which must be considered when extrapolating fission-fragment type damage in current fuels to advanced fuels.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Achieving geometric accuracy in FFT-based micromechanical models using conformal grid

Owing to its efficiency, simplicity and robustness, the FFT-based method has become the standard for computation of mechanical fields in a heterogeneous periodic unit cell. One of the main disadvantages of the FFT-based method is the inaccurate representation of the initial microstructure on a regular grid of voxels, which can be alleviated through the use of distorted initial grids. Here, in this paper, a method for generation of distorted initial grids conforming to the microstructural features (e.g. straight/curved boundaries) is proposed. The method determines the positions of the grid nodes in the initial configuration by solving a system of springs connecting the nodes. Microstructures consisting of layers, Voronoi tessellation and circular/spherical inclusions are considered, and mechanical fields simulated using the FFT-based method. It is found that distorted initial grids, conforming to the microstructural features, lead to more accurate mechanical fields in comparison to the corresponding non-distorted initial grid solution. The effect of initial grid distortion on the convergence of the FFT-based method is analyzed and discussed.

36 MATERIALS SCIENCE↗