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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR)

An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 10 1 to 10 4 viruses per cell, and H1N1 ranging from 10 1 to 10 3 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Microfluidic platform for multiplexed detection in single cells and methods thereof

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

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

A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution

Abstract The cephalopod and vertebrate visual systems are a textbook example of convergent evolution with unknown molecular underpinnings. Here we characterize 98,537 single-cell transcriptomes in the bobtail squidEuprymna berryito understand how the cephalopod retina and optic lobes relate to the vertebrate retina. We confirm the overall relative simplicity of the cephalopod retina but identify two related photoreceptor cell subtypes expressing distinct r-opsins. By contrast, the adult optic lobe contains a diverse repertoire of neuronal and glial cell types, with a predominance of dopaminergic neurons. We show that cephalopod-specific gene duplicates probably contributed to this cell type diversification. Comparing neuronal cell population in the optic lobes of hatchlings and adults, we reveal a switch towards dopaminergic neurotransmitter usage with age, indicative of a maturation process. We further identify an FMRF-amide-based retrograde signal from the optic lobe towards the retina that supports the functional analogy of the cephalopod optic lobe cortex and the vertebrate inner retina in visual signal processing from a molecular standpoint. Finally, comparative analyses with vertebrate and arthropod cells suggest a scenario in which two photoreceptor types and two neuronal populations may have already been present in the eye of the bilaterian ancestor.

Environmental Sciences & Ecology↗
DOE OSTI2025

Standardization and best practices in single-cell testing for liquid alkaline water electrolysis

The increasing demand for efficient and sustainable hydrogen production has driven significant advancements in water electrolysis technologies. Among these, liquid alkaline water electrolysis (LAWE) stands out for its cost-effectiveness and scalability. This manuscript establishes best practices and standardized testing procedures for single-cell LAWE, focusing on the use of nickel foam as both anode and cathode substrates, while incorporating catalysts such as nickel-iron layered double hydroxide (NiFe-LDH) as the anode material and nickel-molybdenum on carbon (NiMo/C) as the cathode material. By providing detailed guidelines on material preparation, cell assembly, and performance evaluation, this work offers a comprehensive framework to improve reproducibility and ensure consistency. The results demonstrate that applying these best practices minimizes variability across different laboratories and experimental setups, laying the groundwork for more robust comparisons and accelerating progress in LAWE research.

08 HYDROGEN↗
DOE OSTI2020

Switchable resolution in soft x-ray tomography of single cells

The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional imaging technique ideally suited to visualizing and quantifying the internal organization of single cells of varying sizes in a near-native state. The achievable resolution of the soft x-ray microscope is largely determined by the objective lens, but switching between objectives is extremely time-consuming and typically undertaken only during microscope maintenance procedures. Since the resolution of the optic is inversely proportional to the depth of focus, an optic capable of imaging the thickest cells is routinely selected. This unnecessarily limits the achievable resolution in smaller cells and eliminates the ability to obtain high-resolution images of regions of interest in larger cells. Here, we describe developments to overcome this shortfall and allow selection of microscope optics best suited to the specimen characteristics and data requirements. We demonstrate that switchable objective capability advances the flexibility of SXT to enable imaging cells ranging in size from bacteria to yeast and mammalian cells without physically modifying the microscope, and we demonstrate the use of this technology to image the same specimen with both optics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A harmonized protocol to assess the single-cell performance of proton exchange membrane water electrolyzers

The harmonization of testing protocols for proton exchange membrane (PEM) electrolyzers is essential for ensuring accurate and reliable performance assessments and accelerating the development of hydrogen production technologies. This protocol provides a structured approach to PEM electrolyzer setup and testing, incorporating key considerations for test station design and single-cell characterization techniques. Polarization curves and electrochemical impedance spectroscopy (EIS) are detailed, along with best practices from academic and industry research groups to enhance data accuracy and comparability. By addressing material variability and harmonizing testing methodologies, this framework enables more precise evaluations of membrane electrode assemblies and electrolyzer components. Harmonized protocols not only streamline development efforts but also foster collaboration across institutions, ultimately supporting the commercialization of hydrogen solutions through improved stack efficiency and durability.

08 HYDROGEN↗
DOE OSTI2021

Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome-related organelles

Significance Transition metals are of crucial importance for primary productivity; their scarcity limits crop yield in agriculture and carbon sequestration on a global scale. Copper (Cu), iron (Fe), and manganese (Mn) are among the most important trace elements that enable the redox chemistry in oxygenic photosynthesis. The single-celled, eukaryotic green alga Chlamydomonas reinhardtii is a choice experimental system for studying trace metal homeostasis in the context of phototrophy, offering all the advantages of a classical microbial system with a well-characterized photosystem and trace metal metabolism machinery of relevance to plants. This project identifies and differentiates different trace metal storage sites in Chlamydomonas and uncovers the dynamics of trace metal storage and mobilization in situations of fluctuating resources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Single-cell quantification of ribosome occupancy in early mouse development

Translation regulation is critical for early mammalian embryonic development. However, previous studies had been restricted to bulk measurements, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N 6 -methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution

Laser ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging method that has the potential to transform the field of metabolomics. This is in part due to LAESI-MS being an ambient ionization method that requires minimal sample preparation and uses (endogenous) water for in situ analysis. This application note details the employment of the ‘LAESI microscope’ source to perform spatially resolved MS analysis of cells and MS imaging (MSI) of tissues at high spatial resolution. This source configuration utilizes a long-working distance reflective objective that permits both visualization of the sample and a smaller LAESI laser beam profile than conventional LAESI setups. In this work, we analyzed 200 single cells of Allium cepa (red onion) and imaged Fittonia argyroneura (nerve plant) in high spatial resolution using this source coupled to a Fourier transform mass spectrometer for high mass resolution and high mass accuracy metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Excellent performance of 650 MHz single-cell niobium cavity after electropolishing

Electropolishing process and cathodes have undergone modification and optimization for both low- and high-beta 650 MHz five-cell niobium cavities for PIP-II. Cavities treated with these modified electropolishing conditions exhibited smooth surfaces and good performance in baseline tests. Nonetheless, due to administrative constraints on project cavities, maximum gradient performance testing was not conducted. This paper presents a study conducted on a single-cell 650 MHz cavity utilizing the optimized electropolishing conditions, highlighting the maximum performance attained for this specific cavity. The cavity tested at 2 K in a vertical cryostat reached a superior accelerating field gradient of 53.3 MV/m at Q0 of 1.6x1010, which is the highest gradient attained for this type of large-sized cavities.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Single-cell RNA-Seq reveals changes in immune landscape in post-traumatic osteoarthritis

Osteoarthritis (OA) is the most common joint disease, affecting over 300 million people world-wide. Accumulating evidence attests to the important roles of the immune system in OA pathogenesis. Understanding the role of various immune cells in joint degeneration or joint repair after injury is vital for improving therapeutic strategies for treating OA. Post-traumatic osteoarthritis (PTOA) develops in ~50% of individuals who have experienced an articular trauma like an anterior cruciate ligament (ACL) rupture. Here, using the high resolution of single-cell RNA sequencing, we delineated the temporal dynamics of immune cell accumulation in the mouse knee joint after ACL rupture. Our study identified multiple immune cell types in the joint including neutrophils, monocytes, macrophages, B cells, T cells, NK cells and dendritic cells. Monocytes and macrophage populations showed the most dramatic changes after injury. Further characterization of monocytes and macrophages reveled 9 major subtypes with unique transcriptomics signatures, including a tissue resident Lyve1 hi Folr2 hi macrophage population and Trem2 hi Fcrls + recruited macrophages, both showing enrichment for phagocytic genes and growth factors such as Igf1 , Pdgfa and Pdgfc. We also identified several genes induced or repressed after ACL injury in a cell type-specific manner. This study provides new insight into PTOA-associated changes in the immune microenvironment and highlights macrophage subtypes that may play a role in joint repair after injury.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Characterization of the strain-rate–dependent mechanical response of single cell–cell junctions

Cell–cell junctions are essential components in multicellular structures and often experience strains of different magnitudes and rates. However, their mechanical behavior is currently underexplored due to the lack of techniques to quantitatively characterize junctional stress–strain relationships. Here we developed a polymeric microstructure to strain the mutual junction of a single cell pair while simultaneously recording the junction stress and observed previously unseen strain-rate–dependent junction responses. We showed that cytoskeleton growth could relax the stress buildup and prevent junction failure at low strain rates, while high strain rates led to synchronized junction failures at remarkably large strains (over 200%). We expect this platform and our biophysical understanding to form the foundation for the rate-dependent mechanics of cell–cell junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (~50°C; pH~10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ~2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO 2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H + /Na + pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group “OPB41.” We propose to name this bacterium ‘Candidatus Hakubanella thermoalkaliphilus.'

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum

Abstract Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Frequency dependence of BCS and residual resistance using multi-mode measurement of nitrogen-doped single-cell elliptical cavities

Various cavity surface treatments have been found to significantly improve cavity quality factor, Q0, with one such treatment being nitrogen-doping (N-doping). N-doped 1.3 GHz cavities were the first found to exhibit anti-Q slope, the increase of Q0 with accelerating field, Eacc. However, even with the use of the same N-doping recipes, this anti-Q slope behavior has not been realized in sub-GHz frequency cavities. In this study, we measured the Q0 and surface resistance, RS, of our N-doped, single-cell, elliptical cavity for both the 644 MHz fundamental mode (FM) and 1.45 GHz higher-order mode (HOM). As a result of multi-mode measurements, the BCS and residual resistances, the temperature-dependent and temperature-in-dependent RF surface resistances, could be determined without the influence of cavity-to-cavity surface treatment variations. We will discuss the frequency-dependent behaviors of the BCS and residual resistances.

Accelerator Physics↗
DOE OSTI2021

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling

Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N 2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A ( Candidatus Atelocyanobacterium thalassa ). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N 2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evaluation of Single-Cell Cavities Made of Forged Ingot Niobium at Jefferson Lab

Currently, fine grain niobium (Nb) (grain size ~ 50 um) and large grain Nb (grain size of a few cm) are being used for the fabrication of superconducting radio frequency (SRF) cavities. Medium grain forged ingot with grain size of a few hundred um may be beneficial for cost-effectiveness as well as providing better performance for future SRF-based accelerators. Forged ingot Nb with medium grain size is a novel production method to obtain Nb discs used for the fabrication of superconducting radio frequency cavities. We have fabricated two 1.5 GHz single cell cavities made from forged Nb ingot with a residual resistivity ratio of ~100. The cavities were chemically and mechanically polished and heat-treated in the temperature range of 650-1000 C before the rf test. One of the cavities reached an accelerating gradient of 34 MV/m with a quality factor Q > 1e10, while the second cavity was limited at 14 MV/m, likely due to a weld defect at the equator.

Dhakal, P.↗