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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate

If biochar is to be used for carbon (C) management, we must understand how weathering or ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550°C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was accelerated via three different processes, namely, (a) physical ageing–subjecting biochar to alternating freeze-thaw and wet-dry cycles, (b) chemical ageing–treating biochar with concentrated hydrogen peroxide and (c) biological ageing–incubating biochar in the presence of nutrients and microorganisms. Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Biochar C mineralization between ageing treatments was significantly different in the case of 350°C biochar ( p value = 0.03). Among the 350°C biochars, physical ageing resulted in the greatest increase (by 103%) in biochar C mineralization ( p value = 0.05). However, in the case of 550°C biochar, ageing did not result in a significant change in biochar C mineralization ( p value = 0.40). Biochar C mineralization was positively correlated with an increase in O/C ratio post-ageing ( r s = 0.86, p value = 0.01). In the case of 350°C biochar, surface oxidation during ageing enhanced biochar degradation by the isolate. For 550°C biochar, however, ageing did not significantly increase biochar C mineralization, likely due to high condensed aromatic C content and lower surface oxidation during ageing. The results from our study suggest that low temperature aged biochar is more susceptible to biological degradation by soil microbes. These findings have implications for the use of biochar for long term C storage in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Synthetic Microbial Consortium for Biological Breakdown and Conversion of Lignin

The plant polymer lignin is the most abundant renewable source of aromatics on the planet and conversion of it to valuable fuels and chemicals is critical to the economic viability of a lignocellulosic biofuels industry and to meeting the DOE’s 2022 goal of $\$2.50$/gallon mean biofuel selling price. Presently, there is no efficient way of converting lignin into valuable commodities. Current biological approaches require mixtures of expensive ligninolytic enzymes and engineered microbes. This project was aimed at circumventing these problems by discovering commensal relationships among fungi and bacteria involved in biological lignin utilization and using this knowledge to engineer microbial communities capable of converting lignin into renewable fuels and chemicals. Essentially, we aimed to learn from, mimic and improve on nature. We discovered fungi that synergistically work together to degrade lignin, engineered fungal systems to increase expression of the required enzymes and engineered organisms to produce products such as biodegradable plastics precursors.

09 BIOMASS FUELS↗
DOE OSTI2022

Biosensor and optogenetics for systems biology of yeast branched-chain alcohol production and tolerance

In this project we combined synthetic biology, systems biology, protein engineering and metabolic engineering to study, control, and improve the production of branched chain alcohols (BCAs), a class of advanced biofuels preferred by the DOE, in the yeast Saccharomyces cerevisiae. This involved the development and application of optogenetic systems as a new modality of dynamic control of native and engineered metabolic pathways, using light as inducible or repressible agent. The optogenetic systems include gene circuits for light control of gene expression, as well as light-assembled synthetic organelles and photo-switchable protein binders to control metabolic and protein function with light at the protein level. In addition, we developed the first genetically encoded biosensor for BCA production in yeast, which we used to design high throughput assays to identify highly productive strains, pathways, and enzymes. We also showed that this biosensor can be functionally co-expressed with optogenetic circuits in the same strain, raising the possibility of establishing, for the first time, computer-interfaced closed-loop controls of engineered metabolic pathways. The yeast gene deletion library was also utilized to conduct the first systems-level study on BCA toxicity in yeast, which uncovered key fundamental principles of yeast sensitivity and tolerance to these alcohols, allowing us to design highly tolerant strains with increased BCA production. This project, thus comprises the development of several new technologies, which we integrated to make new discoveries on the dynamics of BCA production and their mechanisms of cellular toxicity and tolerance, as well as to establish new paradigms to engineer and control metabolic pathways and microbial fermentations with light, for the production of BCAs and other products of interest to the DOE.

2-metyl-1-butanol↗
DOE OSTI2024

IX Cell Wall Research Conference 2022 (IXCWRC): Cell wall research for new fundamental discoveries and applications in plant biology

This application is for securing funds to offset the registration fees and lodging costs for US-based early career investigators (ERCs) to participate to the IX Cell Wall Research Conference 2022 (IXCWRC 2022): Cell wall research for new fundamental discoveries and applications in plant biology. The conference will be held in East Lansing, Michigan on June 13-17, 2022. The conference will focus on the plant cell wall. Plant cells are encapsulated by the cell wall, a dynamic structure that protects them, enables them to interface with the external environment and supports the growth of the entire organism. There is a growing interest in understanding the complex processes necessary to build and deconstruct the plant cell wall. A better understanding of how the cell wall is synthesized during plant growth and in response to the environment, and how it is deconstructed for a broad variety of applications can inform and improve biotechnological processes for increasing biomass yield and improving industrial processes for the recovery of valuable, sustainable polymers. Acquiring such knowledge requires the exchange of new ideas and results as well as the development and application of new technologies. The IXCWRC 2022 aims to reach this goal by providing an opportunity for an open forum to discuss new ideas and theories and develop collaborations for scientists across the globe in a diverse and supportive environment. A distinction of the IXCWRC 2022 from all the preceding plant cell wall conferences will be its focus on the training and inclusion of the next generation of scientists, the ERCs. The overall goal of this application is to broaden the participation of ERCs with a focus on underrepresented communities. The specific goal of this application is to secure support for registration and lodging for US-based ERCs to attend the conference. Priority will be given to ERCs from underrepresented communities in science. We expect that support from DOE will allow the development of an exciting and innovative program to discuss the latest scientific advances in cell wall biology research, advance the next generation of plant cell wall researchers and foster the foundations of an inclusive community in science.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biological Electron Transfer and Catalysis EFRC

The focus of the Biological Electron Transfer and Catalysis (BETCy) EFRC research is elucidating mechanisms of conversion of electrochemical potential into chemical bond energy and is organized into two integrated Thrusts: Electron Bifurcation Catalysis and Electron Transfer Kinetics. We are developing a collective knowledge of metalloenzymes as models for redox reactions by applying physical science and computational tools to characterize biochemical reactions catalyzed by multi- subunit enzymes harboring arrays of iron-sulfur clusters and flavin cofactors. Understanding these mechanisms is central to overcoming the thermodynamic barriers that currently limit production of reduced products and fuels. Biological systems have elegant strategies for converting electrochemical potential energy into chemical bond energy (e.g., C-H, H-H, and N-H) stored in reduced compounds that can serve as advanced biofuels. One significant limitation for the production of highly reduced compounds is that their production in natural and industrial processes relies on low oxidation-reduction potential chemicals as feedstocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach (Final Report)

SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach In the SyPro Poplar project, we aimed to integrate omics, bioinformatics, synthetic biology, and genetic engineering approaches to develop transgenic poplar trees with sustained photosynthetic activity and increased biomass production under individual and the simultaneous occurrence of water deficit, increased soil salinity, and elevated temperatures. Specifically, we intended to (i) study the functions of selected stress-responsive genes at tissue and cell type-specific levels, (ii) discover novel motifs and construct stress-responsive synthetic promoters, and (iii) use these promoters to drive the expression of genes shown to confer abiotic stress tolerance in a variety of crops and develop abiotic stress-tolerant poplars in a coordinated fashion.

09 BIOMASS FUELS↗
DOE OSTI2024

A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports large-scale data generation efforts across its two divisions: Biological Systems Science and Earth and Environmental Systems Sciences. These efforts include user facilities in atmospheric radiation measurements, genomics, metabolomics, proteomics, compute, and imaging. In addition, BER supports the development of plant-based fuels; research in biosystems design, environmental microbiomes, and atmospheric systems; energy flux monitoring; climate-based ecosystem experiments; pathogen biopreparedness; and modeling of climate, urban interfaces, and interactions between people and energy resources. For data access, BER supports community data services at its user facilities, along with specialized data initiatives for Earth and environmental science, climate modeling, genomic and microbial analysis, and multisector dynamics modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Limits on the Evolutionary Rates of Biological Traits

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait’s average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher’s fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-of relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species’ weights to the lengths of DNA strands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Salk Institute for Biological Studies Requirements (Analysis Report)

EPOC uses the Deep Dive process to discuss and analyze current and planned science, research, or education activities and the anticipated data output of a particular use case, site, or project to help inform the strategic planning of a campus or regional networking environment. This includes understanding future needs related to network operations, network capacity upgrades, and other technological service investments. A Deep Dive comprehensively surveys major research stakeholders’ plans and processes in order to investigate data management requirements over the next 5–10 years. Between February and March 2024, staff members from the Engagement and Performance Operations Center (EPOC) met with researchers and staff from the Salk Institute for Biological Studies (Salk) for the purpose of a Deep Dive into scientific and research drivers. The goal of this activity was to help characterize the requirements for a number of campus use cases, and to enable cyberinfrastructure support staff better to understand the needs of the researchers within the community. Material for this event included the written documentation from each of the profiled research areas, documentation about the current state of technology support, and a write-up of the discussion that took place via e-mail and video conferencing. The case studies highlighted the ongoing challenges and opportunities that Salk Institute for Biological Studies have in supporting a cross-section of established and emerging research use cases. Each case study mentioned unique challenges which were summarized into common needs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Functional characterization of glycosyltransferases in duckweed to enable predictive biology

Glycosyltransferases (GTs) catalyze the formation of glycosidic linkages to produce almost all complex carbohydrates. This project used a multi-disciplinary, high-throughput (HTP) biochemical and computational biology approach focused on duckweed as a model energy crop, to study carbohydrate metabolic processes. To achieve this, developed and carried out out high-throughput (HTP) functional characterization of plant glycosyltransferases (GTs) role of enzymatic microenvironments be assessed through a combined proteomic and computational biology approach, and the combined data was used to populate deep-learning frameworks to predict plant GT function. Functional validation achieved through this research is being used to assign gene function and study plant processes at the systems level to efficiently link the genome sequence with gene function. Together, the combined approaches used within this study provide a foundation for how computational prediction, in combination with high-throughput functional validation, can be used to study plant processes at the systems level and translate knowledge gained to efficiently link genome sequence with gene function in a species agnostic manner.

09 BIOMASS FUELS↗
DOE OSTI2023

Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC

Introduction: Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate. Methods: 16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina. Results: We found that methane began to accumulate while sulfate is still abundant (6–8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES). Discussion: We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the cooccurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Protein carbamylation and proteomics: from artifacts to elucidation of biological functions

Lysine carbamylation is a non-enzymatic protein post-translational modification (PTM) that plays important roles in regulating enzymatic activity and the pathogenesis of diseases such as atherosclerosis, rheumatoid arthritis, and uremia. The progress of understanding the roles of carbamylation in biological systems has been delayed due to lack of systematic assays to study its functions. To aggravate this scenario, carbamylation is a major artifact in proteomics analysis given that urea, which is used during sample preparation, induces carbamylation. In addition, anti-acetyllysine antibodies co-purify carbamylated and acetylated peptides. In a recent paper, we leveraged co-purification with anti-acetyllysine antibodies to develop a method for analyzing carbamylated proteomes. In this perspective article, we discuss how this method may be applied to characterize the physiological functions of carbamylation in humans and other biological models, as well as the utility of establishing novel disease biomarkers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhanced Monte Carlo Simulations for Electron Energy Loss Mitigation in Real-Space Nanoimaging of Thick Biological Samples and Microchips

High-resolution imaging using Transmission Electron Microscopy (TEM) is essential for applications such as grain boundary analysis, microchip defect characterization, and biological imaging. However, TEM images are often compromised by electron energy spread and other factors. In TEM mode, where the objective and projector lenses are positioned downstream of the sample, electron–sample interactions cause energy loss, which adversely impacts image quality and resolution. This study introduces a simulation tool to estimate the electron energy loss spectrum (EELS) as a function of sample thickness, covering electron beam energies from 300 keV to 3 MeV. Leveraging recent advances in MeV-TEM/STEM technology, which includes a state-of-the-art electron source with 2-picometer emittance, an energy spread of 3 × 10 -5 , and optimized beam characteristics, we aim to minimize energy spread. By integrating EELS capabilities into the BNL Monte Carlo (MC) simulation code for thicker samples, we evaluate electron beam parameters to mitigate energy spread resulting from electron–sample interactions. Based on our simulations, we propose an experimental procedure for quantitively distinguishing between elastic and inelastic scattering. The findings will guide the selection of optimal beam settings, thereby enhancing resolution for nanoimaging of thick biological samples and microchips.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Biological Consequences of Marine Energy Development on Marine Animals

Marine energy devices harness power from attributes of ocean water to form a sustainable energy source. Knowledge gaps remain about whether marine energy systems can affect the environment, adding another threat to animal populations and habitats already under pressure from climate change and anthropogenic activities. To date, potential environmental effects have been studied under the scope of stressor–receptor interactions, where moving parts of, or emissions from, a system could harm the animals, habitats, and natural processes. While crucial for understanding effects and identifying knowledge gaps, this approach misses a holistic view of what animals may experience in the presence of marine energy systems. We look at six biological consequences and forces that drive the health of an animal population and the effects expected from marine energy development: success of early life stages; changes in competitive capabilities; growth and survival based on food availability; susceptibility to predators; injury or death; and reproductive success. We use case studies to develop this approach, focusing on a variety of marine animals. An approximate level of risk is assigned for each interaction based on the biological consequences. This work highlights the need to examine the effects of marine energy development on animal populations within their natural habitats.

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

Structure of Lipopolysaccharide from Liberibacter crescens Is Low Molecular Weight and Offers Insight into Candidatus Liberibacter Biology

Huanglongbing (HLB) disease, also known as citrus greening disease, was first reported in the US in 2005. Since then, the disease has decimated the citrus industry in Florida, resulting in billions of dollars in crop losses and the destruction of thousands of acres of citrus groves. The causative agent of citrus greening disease is the phloem limited pathogen Candidatus Liberibacter asiaticus. As it has not been cultured, very little is known about the structural biology of the organism. Liberibacter are part of the Rhizobiaceae family, which includes nitrogen-fixing symbionts of legumes as well as the Agrobacterium plant pathogens. To better understand the Liberibacter genus, a closely related culturable bacterium (Liberibacter crescens or Lcr) has attracted attention as a model organism for structural and functional genomics of Liberibacters. Given that the structure of lipopolysaccharides (LPS) from Gram-negative bacteria plays a crucial role in mediating host-pathogen interactions, we sought to characterize the LPS from Lcr. We found that the major lipid A component of the LPS consisted of a pentaacylated molecule with a β-6-GlcN disaccharide backbone lacking phosphate. The polysaccharide portion of the LPS was unusual compared to previously described members of the Rhizobiaceae family in that it contained ribofuranosyl residues. The LPS structure presented here allows us to extrapolate known LPS structure/function relationships to members of the Liberibacter genus which cannot yet be cultured. It also offers insights into the biology of the organism and how they manage to effectively attack citrus trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.

60 APPLIED LIFE SCIENCES↗