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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
NASA NTRS2009

A New View of Radiation-Induced Cancer: Integrating Short- and Long-Term Processes. Part II: Second Cancer Risk Estimation

As the number of cancer survivors grows, prediction of radiotherapy-induced second cancer risks becomes increasingly important. Because the latency period for solid tumors is long, the risks of recently introduced radiotherapy protocols are not yet directly measurable. In the accompanying article, we presented a new biologically based mathematical model, which, in principle, can estimate second cancer risks for any protocol. The novelty of the model is that it integrates, into a single formalism, mechanistic analyses of pre-malignant cell dynamics on two different time scales: short-term during radiotherapy and recovery; long-term during the entire life span. Here, we apply the model to nine solid cancer types (stomach, lung, colon, rectal, pancreatic, bladder, breast, central nervous system, and thyroid) using data on radiotherapy-induced second malignancies, on Japanese atomic bomb survivors, and on background US cancer incidence. Potentially, the model can be incorporated into radiotherapy treatment planning algorithms, adding second cancer risk as an optimization criterion.

Shuryak, Igor↗
DOE OSTI2021

Nanoscale biochemical sample preparation and analysis

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

Kelly, Ryan T.↗
DOE OSTI2023

Quantitative elemental imaging in eukaryotic algae

Abstract All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision

Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Previously, we used in situ cryo-electron tomography to reveal the native architecture of thylakoid membranes (Engel et al., 2015). Here, we leverage technical advances to resolve the individual protein complexes within these membranes. Combined with a new method to visualize membrane surface topology, we map the molecular landscapes of thylakoid membranes inside green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SIVB's 2024 In Vitro Biology Meeting Proceedings

SIVB's 2024 World Congress on In Vitro Biology took place in Saint Louis, Missouri, from June 8th to 12th, 2024. The conference featured renowned speakers from academic and non-academic institutions who will present recent advancements in critical areas like plant transformation, genome editing, synthetic biology, advanced breeding technologies, cellular agriculture, future food sources, chromosome engineering, epigenetics, artificial intelligence, and machine learning. The Society for In Vitro Biology (SIVB) has always considered the education and professional development of young researchers as an integral component of its mission. The 2024 World Congress program, along with SIVB’s student initiatives, was customized to foster scientific growth and professional development among students and young scientists empowering them in their professional journeys. The recording of the DOE supported "Single Cell RNA Sequencing" workshop was made publicly available at https://youtu.be/A0UnuYwefwg for easy retrieval and reference of all information shared during the live event, thereby increasing accessibility and knowledge transfer. Their are 14 articles in the proceedings and the full list of files is located at https://link.springer.com/journal/11626/volumes-and-issues/60-1/supplement.

10 SYNTHETIC FUELS↗
NASA NTRS2001

Cell-cycle research with synchronous cultures: an evaluation

The baby-machine system, which produces new-born Escherichia coli cells from cultures immobilized on a membrane, was developed many years ago in an attempt to attain optimal synchrony with minimal disturbance of steady-state growth. In the present article, we put forward a model to describe the behaviour of cells produced by this method, and provide quantitative evaluation of the parameters involved, at each of four different growth rates. Considering the high level of selection achievable with this technique and the natural dispersion in interdivision times, we believe that the output of the baby machine is probably close to optimal in terms of both quality and persistence of synchrony. We show that considerable information on events in the cell cycle can be obtained from populations with age distributions very much broader than those achieved with the baby machine and differing only modestly from steady state. The data presented here, together with the long and fruitful history of findings employing the baby-machine technique, suggest that minimisation of stress on cells is the single most important factor for successful cell-cycle analysis.

Non-NASA Center↗
NASA NTRS2009

Biomorphic Multi-Agent Architecture for Persistent Computing

A multi-agent software/hardware architecture, inspired by the multicellular nature of living organisms, has been proposed as the basis of design of a robust, reliable, persistent computing system. Just as a multicellular organism can adapt to changing environmental conditions and can survive despite the failure of individual cells, a multi-agent computing system, as envisioned, could adapt to changing hardware, software, and environmental conditions. In particular, the computing system could continue to function (perhaps at a reduced but still reasonable level of performance) if one or more component( s) of the system were to fail. One of the defining characteristics of a multicellular organism is unity of purpose. In biology, the purpose is survival of the organism. The purpose of the proposed multi-agent architecture is to provide a persistent computing environment in harsh conditions in which repair is difficult or impossible. A multi-agent, organism-like computing system would be a single entity built from agents or cells. Each agent or cell would be a discrete hardware processing unit that would include a data processor with local memory, an internal clock, and a suite of communication equipment capable of both local line-of-sight communications and global broadcast communications. Some cells, denoted specialist cells, could contain such additional hardware as sensors and emitters. Each cell would be independent in the sense that there would be no global clock, no global (shared) memory, no pre-assigned cell identifiers, no pre-defined network topology, and no centralized brain or control structure. Like each cell in a living organism, each agent or cell of the computing system would contain a full description of the system encoded as genes, but in this case, the genes would be components of a software genome.

Lodding, Kenneth N.↗
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↗
NASA NTRSDate not supplied

The BioSensor Instrument Beyond LEIA: a Versatile Platform for Lunar Biology

Introduction: The BioSensor is a deep-space-compatible automated microfluidic culturing instrument. While originally designed to measure the effects of deep space radiation on yeast growth for the BioSentinel mission, it has the potential to host a diverse range of life science experiments with single- and/or multi-celled organisms and can be adapted to interface with a diverse range of platforms in both crewed and uncrewed settings. It is therefore a leading candidate for hosting life sciences experimentation associated with a lunar surface habitat. BioSensor design: The function of the BioSensor is to monitor the growth and metabolic activity of samples in batch fluidic culture, without the need for crew involvement. The current configuration houses organisms in 16 wells within 16 microfluidic cards, accommodating a total of 256 samples, replicates, and controls. Each well has an optical system including three LEDs and a photodiode detector to measure absorbance at three wavelengths, enabling measurement of optical density, color change in dyes such as alamarBlue, and bioproduction of pigmented compounds. Organisms are loaded into fluidic wells and air-dried for storage during integration, launch, and transit, then activated by the introduction of culture medium from storage bags via manifolds that fill one card at a time. Temperature is controlled by individual card heaters, and timing of all activities (fluidics fills, optical measurements, temperatures) is directed by an experiment script. The self-contained BioSensor payload is roughly 4U in volume; with electrical/mechanical/thermal interface, e.g. for operation on ISS or a lunar lander, as well as a linear energy-transfer (LET) charged-particle radiation spectrometer, the entire system is closer to 6U. BioSentinel and LEIA: Flown on the ISS and in a deep-space free flyer for BioSentinel, the BioSensor has been modified for use in the LEIA mission, including improvements to reduce the sensitivity to lengthy launch delays. LEIA will monitor yeast growth in the radiation and reduced-gravity environment of the lunar surface no earlier than 2026, on a CLPS lander [4]. Changes include accommodating additional culture media and an additional LED color for a new biological assay (bioproduction of carotenoids-- dietary antioxidants), as well as modifications to the housing to allow late-load biology changeout and improved isolation between fluidics and electronics. Future prospects: Future work with the BioSensor, beyond LEIA, will include expanding the range and diversity of organisms and assays accommodated. Preliminary work has demonstrated the growth of Arabidopsis seedlings in BioSensor fluidic cards, including optical measurements of growth rate over time. Minor modifications could allow measurement of phenotypes related to photosynthetic capacity in both plants and cyanobacteria. The experimental capabilities of the BioSensor could be dramatically increased by introducing the capability for fluorescence measurements, and/or the design of novel biological assays using luminescence. The BioSensor can also be adapted for new platforms and experiment settings; in addition to free-flyer, ISS, and CLPS lander, a preliminary design concept has been developed for crewed deployment directly to the lunar surface. The instrument could be accommodated inside a lunar habitat, where its automated operation would make it an excellent candidate for experiments from fundamental investigations into the response of organisms to lunar surface conditions to applied-science purposes such as screening engineered strains of various organisms for bioproduction capability.

J A Lee↗
DOE OSTI2023

Using Methyl Bromide for Interspecies Cell–Cell Signaling and As a Reporter in a Model Soil Consortium

Synthetic microbial communities are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five member MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that Variovorax beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally-relevant hydration conditions. We find that methyl halide production can report on a MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. Finally, these tools will be useful for future studies that investigate how MSC respond to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Nanobodies against the metal binding domains of ATP7B as tools to study copper transport in the cell

Abstract Nanobodies are genetically engineered single domain antibodies derived from the unusual heavy-chain only antibodies found in llamas and camels. The small size of the nanobodies and flexible selection schemes make them uniquely versatile tools for protein biochemistry and cell biology. We have developed a panel of nanobodies against the metal binding domains of the human copper transporter ATP7B, a multidomain membrane protein with a complex regulation of enzymatic activity and intracellular localization. To enable the use of the nanobodies as tools to investigate copper transport in the cell, we characterized their binding sites and affinity by isothermal titration calorimetry and NMR. We have identified nanobodies against each of the first four metal binding domains of ATP7B, with a wide affinity range, as evidenced by dissociation constants from below 10−9 to 10−6 M. We found both the inhibitory and activating nanobodies among those tested. The diverse properties of the nanobodies make the panel useful for the structural studies of ATP7B, immunoaffinity purification of the protein, modulation of its activity in the cell, protein dynamics studies, and as mimics of copper chaperone ATOX1, the natural interaction partner of ATP7B.

Uhlemann, Eva-Maria E.↗
NASA NTRS1996

Theories and models on the biological of cells in space

A wide variety of observations on cells in space, admittedly made under constraining and unnatural conditions in may cases, have led to experimental results that were surprising or unexpected. Reproducibility, freedom from artifacts, and plausibility must be considered in all cases, even when results are not surprising. The papers in symposium on 'Theories and Models on the Biology of Cells in Space' are dedicated to the subject of the plausibility of cellular responses to gravity -- inertial accelerations between 0 and 9.8 m/sq s and higher. The mechanical phenomena inside the cell, the gravitactic locomotion of single eukaryotic and prokaryotic cells, and the effects of inertial unloading on cellular physiology are addressed in theoretical and experimental studies.

Todd, P.↗
NASA NTRS2003

Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

NASA Program Biological Systems Research↗
DOE OSTI2022

Mixed heavy metal stress induces global iron starvation response

Abstract Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Enabling reactive microscopy with MicroMator

Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods and improved computational resources. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Applications in which reactiveness is needed are multifarious. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments. It provides a Python software environment and an extensible set of modules that greatly facilitate the definition of events with triggers and effects interacting with the experiment. We provide a pedagogic example performing dynamic adaptation of fluorescence illumination on bacteria, and demonstrate MicroMator’s potential via two challenging case studies in yeast to single-cell control and single-cell recombination, both requiring real-time tracking and light targeting at the single-cell level.

47 OTHER INSTRUMENTATION↗
NASA NTRS2014

Radiation Quality Effects on Transcriptome Profiles in 3-d Cultures After Particle Irradiation

In this work, we evaluate the differential effects of low- and high-LET radiation on 3-D organotypic cultures in order to investigate radiation quality impacts on gene expression and cellular responses. Reducing uncertainties in current risk models requires new knowledge on the fundamental differences in biological responses (the so-called radiation quality effects) triggered by heavy ion particle radiation versus low-LET radiation associated with Earth-based exposures. We are utilizing novel 3-D organotypic human tissue models that provide a format for study of human cells within a realistic tissue framework, thereby bridging the gap between 2-D monolayer culture and animal models for risk extrapolation to humans. To identify biological pathway signatures unique to heavy ion particle exposure, functional gene set enrichment analysis (GSEA) was used with whole transcriptome profiling. GSEA has been used extensively as a method to garner biological information in a variety of model systems but has not been commonly used to analyze radiation effects. It is a powerful approach for assessing the functional significance of radiation quality-dependent changes from datasets where the changes are subtle but broad, and where single gene based analysis using rankings of fold-change may not reveal important biological information. We identified 45 statistically significant gene sets at 0.05 q-value cutoff, including 14 gene sets common to gamma and titanium irradiation, 19 gene sets specific to gamma irradiation, and 12 titanium-specific gene sets. Common gene sets largely align with DNA damage, cell cycle, early immune response, and inflammatory cytokine pathway activation. The top gene set enriched for the gamma- and titanium-irradiated samples involved KRAS pathway activation and genes activated in TNF-treated cells, respectively. Another difference noted for the high-LET samples was an apparent enrichment in gene sets involved in cycle cycle/mitotic control. It is plausible that the enrichment in these particular pathways results from the complex DNA damage resulting from high-LET exposure where repair processes are not completed during the same time scale as the less complex damage resulting from low-LET radiation.

Patel, Z. S.↗
DOE OSTI2024

The Gene Fitness Atlas: A Roadmap for Predicting Evolution

We developed a novel, high-throughput microfluidic device design containing “interaction zones” where progeny cell lines compete against each other allowing for accurate analysis of bacterial cell fitness. The goal of the project was to use the device for two applications: 1) gene knockout screening and 2) antibiotic resistance screening. The microfluidic platform was fabricated using photolithography and soft lithography in polydimethylsiloxane (PDMS). E.coli Keio mutants and fluorescent wildtype parent were chosen for the study. Cells were grown overnight and their loading into the devices and seeding in mother machines was optimized. For mutant screening, the least fit mutant and wildtype parent were cultured individually and then added to the microfluidic device. The mother machines which were seeded with mutant and wildtype were imaged through time lapse microscopy and the growth of cells was observed. For antibiotic screening, wildtype E.coli cells which were grown overnight were added to the device and washed with media containing the antibiotic ampicillin. The growth pattern in presence and absence of ampicillin was observed through time lapse microscopy. It was observed that over a period of four hours, both the mutant and the wildtype divided in the mother machine and pushed daughter cells out into the interaction zone. In case of the antibiotic screening experiment, the fluorescent wildtype divided both in the absence and presence of sublethal concentration of ampicillin. This study is a proof of concept demonstration of high- throughput single cell analysis of cells using a novel microfluidics device.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

Analysis of cell mechanics in single vinculin-deficient cells using a magnetic tweezer

A magnetic tweezer was constructed to apply controlled tensional forces (10 pN to greater than 1 nN) to transmembrane receptors via bound ligand-coated microbeadswhile optically measuring lateral bead displacements within individual cells. Use of this system with wild-type F9 embryonic carcinoma cells and cells from a vinculin knockout mouse F9 Vin (-/-) revealed much larger differences in the stiffness of the transmembrane integrin linkages to the cytoskeleton than previously reported using related techniques that measured average mechanical properties of large cell populations. The mechanical properties measured varied widely among cells, exhibiting an approximately log-normal distribution. The median lateral bead displacement was 2-fold larger in F9 Vin (-/-) cells compared to wild-type cells whereas the arithmetic mean displacement only increased by 37%. We conclude that vinculin serves a greater mechanical role in cells than previously reported and that this magnetic tweezer device may be useful for probing the molecular basis of cell mechanics within single cells. Copyright 2000 Academic Press.

Non-NASA Center↗