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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 OSTI2023

Motility of Synthetic Cells from Engineered Lipids

Synthetic cells are artificial systems that resemble natural cells. Significant efforts have been made over the years to construct synthetic protocells that can mimic biological mechanisms and perform various complex processes. These include compartmentalization, metabolism, energy supply, communication, and gene reproduction. Cell motility is also of great importance, as nature uses elegant mechanisms for intracellular trafficking, immune response, and embryogenesis. In this review, we discuss the motility of synthetic cells made from lipid vesicles and relevant molecular mechanisms. Synthetic cell motion may be classified into surface-based or solution-based depending on whether it involves interactions with surfaces or movement in fluids. Collective migration behaviors have also been demonstrated. The swarm motion requires additional mechanisms for intercellular signaling and directional motility that enable communication and coordination among the synthetic vesicles. In addition, intracellular trafficking for molecular transport has been reconstituted in minimal cells with the help of DNA nanotechnology. These efforts demonstrate synthetic cells that can move, detect, respond, and interact. Finally, we envision that new developments in protocell motility will enhance our understanding of biological processes and be instrumental in bioengineering and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Epigenetic Regulation by Polycomb Complexes from Drosophila to Human and Its Relation to Communicable Disease Pathogenesis

Although all cells in the human body are made of the same DNA, these cells undergo differentiation and behave differently during development, through integration of external and internal stimuli via ‘specific mechanisms.’ Epigenetics is one such mechanism that comprises DNA/RNA, histone modifications, and non-coding RNAs that regulate transcription without changing the genetic code. The discovery of the first Polycomb mutant phenotype in Drosophila started the study of epigenetics more than 80 years ago. Since then, a considerable number of Polycomb Group (PcG) genes in Drosophila have been discovered to be preserved in mammals, including humans. PcG proteins exert their influence through gene repression by acting in complexes, modifying histones, and compacting the chromatin within the nucleus. In this article, we discuss how our knowledge of the PcG repression mechanism in Drosophila translates to human communicable disease research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Systemic stomatal responses in plants: Coordinating development, stress, and pathogen defense under a changing climate

To successfully survive, develop, grow and reproduce, multicellular organisms must coordinate their molecular, physiological, developmental and metabolic responses among their different cells and tissues. This process is mediated by cell-to-cell, vascular and/or volatile communication, and involves electric, chemical and/or hydraulic signals. Within this context, stomata serve a dual role by coordinating their responses to the environment with their neighbouring cells at the epidermis, but also with other stomata present on other parts of the plant. As stomata represent one of the most important conduits between the plant and its above-ground environment, as well as directly affect photosynthesis, respiration and the hydraulic status of the plant by controlling its gas and vapour exchange with the atmosphere, coordinating the overall response of stomata within and between different leaves and tissues plays a cardinal role in plant growth, development and reproduction. Here, we discuss different examples of local and systemic stomatal coordination, the different signalling pathways that mediate them, and the importance of systemic stomatal coordination to our food supply, ecosystems and weather patterns, under our changing climate. Importantly, we further discuss the potential biotechnological implications of regulating systemic stomatal responses for enhancing agricultural productivity in a warmer and CO 2 -rich environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗
DOE OSTI2023

System and method for three-dimensional in vitro flexible microelectrode array

The present disclosure relates to a biocompatible, in vitro probe system. The probe system may have a substrate and a culture well supported on the substrate. The culture well defines a three-dimensional volume for containing in vitro cultures of electroactive cells. The probe system has at least one probe subsystem supported on the substrate. The probe subsystem has at least one probe having an array of electrodes, with the probe being disposed within the culture well for in vitro electrically communicating with the electroactive cells. The probe subsystem is adapted to be interfaced to an external instrumentation/recording device.

Soscia, David↗
DOE OSTI2026

Detailed Method for the Purification of Rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana

The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana . Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species.

25 ENERGY STORAGE↗
DOE OSTI2020

Performance Evaluation of a Two-Dimensional Flood Model on Heterogeneous High-Performance Computing Architectures

This paper describes the implementation of a two-dimensional hydrodynamic flood model with two different numerical schemes on heterogeneous high-performance computing architectures. Both schemes were able to solve the nonlinear hyperbolic shallow water equations using an explicit upwind first-order approach on finite differences and finite volumes, respectively, and were conducted using MPI and CUDA. Four different test cases were simulated on the Summit supercomputer at Oak Ridge National Laboratory. Both numerical schemes scaled up to 128 nodes (768 GPUs) with a maximum 98.2x speedup of over 1 GPU. The lowest run time for the 10 day Hurricane Harvey event simulation at 5 meter resolution (272 million grid cells) was 50 minutes. GPUDirect communication proved to be more convenient than the standard communication strategy. Both strong and weak scaling are shown.

Sharif, Md Bulbul↗
DOE OSTI2024

Chloroplast Stress Signals: Control of Retrograde Signaling, Chloroplast Turn-Over, and Cell Fate Decisions

Chloroplasts (photosynthetic plastids) are semiautonomous organelles that contain their own small genomes. The proteomes of chloroplasts, however, are a mixture of plastid and nuclear-encoded proteins. Chloroplasts perform photosynthesis, which is prone to damaging the organelles, leading to the production of reactive oxygen species (ROS) that damage the cell under environmental stresses. Thus, for the cell to maintain proper chloroplast function, efficient photosynthesis, and avoid ROS damage, it relies on complex crosstalk between the chloroplast, the nucleus, other organelles within the cell, and the cytoplasm in between. This communication involves retrograde signals from chloroplasts to control nuclear gene expression, programmed cell death (PCD), and chloroplast degradation. Here we review these signals with an emphasis on the roles of the ROS singlet oxygen ( 1 O 2 ) and plastid gene expression. We cover (1) recent work on understanding how multiple 1 O 2 signaling pathways can be initiated within stressed chloroplasts, (2) how individualized post-translational regulatory systems allow chloroplasts to control their proteomes and degradation, and (3) how chloroplast signals ultimately control cell fate decisions, such as PCD, senescence, and vacuole-mediated degradation of chloroplasts (chloroplast quality control). Overall, this chapter discusses how chloroplasts can act as environmental sensors for the cell and allow plants to acclimate to stress and thrive in dynamic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nematic cell alignment directs calcium waves in an epithelial monolayer

Tissues rely on supracellular signals to coordinate their cells over a long range. Two such tissuescale cues are calcium waves and patterns of cell-cell alignment or nematic order. During wound healing, for example, calcium waves propagate across a tissue to guide directed cell migration and reepithelialization. Defects in long-range cell-cell alignment, or nematic orientation, can act to localize morphogenetic events in a tissue. Although these two cues have been considered in isolation, we demonstrate a relationship in epithelial tissue between long-range calcium signaling and the cell’s nematic order: The speed of a wound-induced calcium wave depends monotonically on the angle between the wave vector and cell axis, with maximal wave speed occurring perpendicular to the tissue’s orientation. Including anisotropic di↵usive coupling between cells in a canonical reactiondi↵usion model recapitulates our measured calcium wave dynamics. Our model demonstrates how orientation defects can desynchronize information propagation across a tissue. A calcium wave front is bent around nematic defects, therefore cells the same distance from a wound can receive the calcium signal at di↵erent times. Our work elucidates how spatial patterns in global cell alignment can control collective communication via calcium signaling during development, wound healing, and disease.

Winterstrain, Annemarie C. [Brandeis University, W↗
DOE OSTI2024

A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

Beneficial symbiotic fungi colonize plant tissues, delivering crucial ecosystem services such as carbon sequestration and plant fertilization. Specifically, trees that form a nutrient-acquiring symbiosis with mutualistic ectomycorrhizal (ECM) fungi gain advantages from these associations by experiencing enhanced growth rates and increased resilience to both biotic and abiotic stresses. Despite the vital role ECM fungi play in the nutrition and well-being of trees, identifying key regulators participating in the molecular communication between plant and fungal cells is still in its early stages. The mutualistic relationship between Laccaria bicolor and Populus spp. has been utilized as a model system for investigating ECM symbiosis at the molecular level. It has been demonstrated that the fungus L. bicolor secretes Mycorrhiza-induced Small Secreted Proteins (MiSSPs) required for ECM development. Meanwhile, we have previously shown that P. trichocarpa small, secreted proteins (PtSSPs) are highly induced during mutualistic symbiosis and some of them can enter, via in-vitro feeding, L. bicolor hyphae affecting their growth and morphology. However, the exact role and mode of action of PtSSPs in mutualistic symbiosis remain unknown. Because previous study showed that PtSSP1 is taking up by fungal cell and then localize in fungal cells, we decide to dig further on its putative role in fungal cells and also by overexpressing it in poplar because it is not technically possible yet to overexpress poplar protein in Laccaria bicolor hyphae. Here, we further characterized the function of PtSSP1(Potri.009G063200) in ectomycorrhization, which accumulates in the nucleus of L. bicolor in an in-vitro feeding experiment. Our results provide new knowledge for the genetic engineering of plants to control associated microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Syncytia in Fungi

Filamentous fungi typically grow as interconnected multinucleate syncytia that can be microscopic to many hectares in size. Mechanistic details and rules that govern the formation and function of these multinucleate syncytia are largely unexplored, including details on syncytial morphology and the regulatory controls of cellular and molecular processes. Recent discoveries have revealed various adaptations that enable fungal syncytia to accomplish coordinated behaviors, including cell growth, nuclear division, secretion, communication, and adaptation of the hyphal network for mixing nuclear and cytoplasmic organelles. In this review, we highlight recent studies using advanced technologies to define rules that govern organizing principles of hyphal and colony differentiation, including various aspects of nuclear and mitochondrial cooperation versus competition. We place these findings into context with previous foundational literature and present still unanswered questions on mechanistic aspects, function, and morphological diversity of fungal syncytia across the fungal kingdom.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Neuromuscular Junction Model Optimized for Electrical Platforms

Neuromuscular junctions (NMJs), specialized synapses between motor neurons and muscle fibers, are essential for muscle activity. A simple and reproducible cell-based in vitro NMJ platform is needed to test the impact of chemicals on the neuron-muscle communication. Our platform utilizes genetically modified neurons and muscle cells, optimized culture conditions, and commercially available multielectrode array system for recording action potentials. Neuronal cells (NSC34) were optogenetically modified with channelrhodopsin chimera to allow for simultaneous, light-mediated, millisecond-precise activation of neuronal population. This signal is propagated through functional synapses to the muscle fibers. Muscle cells (C2C12) were modified by incorporating gap junction protein (Connexin-43) to improve intracellular communication without affecting muscle differentiation. This communication between muscle fibers resulted in better signal propagation and signal strength. Optimized culture medium facilitated the growth and differentiation of both cell types together. Our system was validated using vecuronium, a muscle relaxant, which abolished the muscle response. This in vitro model provides a unique tool for establishing a NMJ platform that is easy to record and analyze. Potential applications include nondestructive long-term screening of drugs affecting the NMJ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles

Extracellular vesicles (EVs) are membrane-bound particles secreted by cells, playing crucial roles in intercellular communication. The composition of EVs can undergo changes in response to stress and disease conditions, making them excellent biomarker candidates. However, extracting protein information from EVs can be challenging due to their low abundance in complex biofluids and copurification with contaminant proteins and particles. Techniques to enrich EVs have their strengths and limitations, without one being able to purify EVs to complete homogeneity. This can lead to compromised recovery rates and increased complexity, making data interpretation difficult. In this viewpoint article, we explore the concept that better characterization of EV composition, followed by quantification of EV proteins in complex samples, might be a more viable route for biomarker development. Mass spectrometers can provide reproducible deep coverage of the EV proteome, despite sample impurities. This paradigm shift presents opportunities to integrate advanced bioinformatics tools to refine the EV proteome landscape, identify novel biomarkers, and streamline validation processes in biomarker development. By focusing on leveraging technology rather than achieving absolute purity, this approach can transform current practices and open opportunities for robust biomarker discovery. Herein, we highlight not only such opportunities but also challenges to implement this concept.

Dakup, Panshak P. [Pacific Northwest National Labo↗
DOE OSTI2023

Coupled Lattice Boltzmann Modeling Framework for Pore-Scale Fluid Flow and Reactive Transport

In this paper, we propose a modeling framework for pore-scale fluid flow and reactive transport based on a coupled lattice Boltzmann model (LBM). We develop a modeling interface to integrate the LBM modeling code parallel lattice Boltzmann solver and the PHREEQC reaction solver using multiple flow and reaction cell mapping schemes. The major advantage of the proposed workflow is the high modeling flexibility obtained by coupling the geochemical model with the LBM fluid flow model. Consequently, the model is capable of executing one or more complex reactions within desired cells while preserving the high data communication efficiency between the two codes. Meanwhile, the developed mapping mechanism enables the flow, diffusion, and reactions in complex pore-scale geometries. We validate the coupled code in a series of benchmark numerical experiments, including 2D single-phase Poiseuille flow and diffusion, 2D reactive transport with calcite dissolution, as well as surface complexation reactions. The simulation results show good agreement with analytical solutions, experimental data, and multiple other simulation codes. In addition, we design an AI-based optimization workflow and implement it on the surface complexation model to enable increased capacity of the coupled modeling framework. Compared to the manual tuning results proposed in the literature, our workflow demonstrates fast and reliable model optimization results without incorporating pre-existing domain knowledge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis

To probe signal propagation and genetic actuation in microbial consortia, we have coopted the components of both redox and quorum sensing (QS) signaling into a communication network for guiding composition by “programming” cell lysis. Here, in this paper, we use an electrode to generate hydrogen peroxide as a redox cue that determines consortia composition. The oxidative stress regulon of Escherichia coli, OxyR, is employed to receive and transform this signal into a QS signal that coordinates the lysis of a subpopulation of cells. We examine a suite of information transfer modalities including “monoculture” and “transmitter-receiver” models, as well as a series of genetic circuits that introduce time-delays for altering information relay, thereby expanding design space. A simple mathematical model aids in developing communication schemes that accommodate the transient nature of redox signals and the “collective” attributes of QS signals. We suggest this platform methodology will be useful in understanding and controlling synthetic microbial consortia for a variety of applications, including biomanufacturing and biocontainment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Open aperture flow cells for on-line optical analysis of process fluids

A flow cell system includes a vessel and a fluid located in the vessel. A fluid surface of the fluid can be vented to a first gas pressure. The fluid surface can have a first cross-sectional area. The flow cell system includes a conduit in fluid communication with the vessel and positioned downstream of the vessel. The conduit can have a region that includes one or more orifices and has a second cross-sectional area. The second cross-sectional area can be less than the first cross-sectional area. The one or more orifices can be vented to a second gas pressure. The second gas pressure can be equal to or greater than the first gas pressure. Methods for analyzing a process fluid can include characterizing the fluid in the conduit.

Launiere, Cari A.↗
DOE OSTI2023

Completion and Testing of a New High-Temperature Cell Holder to Support High Dose Rate Electron Beam Irradiations of Select Sulfur Chlorides (S2Cl2 and SOCl2) for Advanced Low Temperature Chlorination of Zirconium-based Used Nuclear Fuel Cladding

Short communication on the completion and testing of a new high-temperature cell holder to support high dose rate electron beam irradiations of select sulfur chlorides (S2Cl2 and SOCl2) for advanced low temperature chlorination of zirconium-based used nuclear fuel cladding.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗