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At least 1,711 records · Page 95

All sources NASA NTRS DOE OSTI

DOE OSTI2017

Balloon-Borne Full-Column Greenhouse Gas Profiling Field Campaign Report

The vertical distributions of CO2, CH4, and other gases provide important constraints for the determination of terrestrial and ocean sources and sinks of carbon and other biogeochemical processes in the Earth system. The DOE Biological and Environmental Research Program (DOE-BER) and the NOAA Earth System Research Laboratory (NOAA-ESRL) collaborate to quantify the vertically resolved distribution of atmospheric carbon-cycle gases (CO2, and CH4) within approximately 99% of the atmospheric column at the DOE ARM Southern Great Plains Facility in Oklahoma. In 2015, flights were delayed while research at NOAA focused on evaluating sources of systematic errors in the gas collection and analysis system and modifying the sampling system to provide duplicate air samples in a single flight package. In 2017, we look forward to proposing additional sampling and analysis at ARM-SGP (and other sites) that characterize the vertical distribution of CO2 and CH4 over time and space.

Community Earth System Model, Southern Great Plain↗

DOE OSTI2021

Cyanobacteriochromes active in the far-red to near-infrared

The present invention provides a protein fusion construct comprising a far-red cyanobacteriochrome (CBCR) domain linked to a heterologous domain, wherein the far-red CBCR domain comprises a CBCR polypeptide and a tetrapyrrole chromophore. The invention also provides nucleic acids, expression cassettes, vectors, and host cells for expression of the far-red CBCR protein fusion constructs. Methods for detecting cellular components, methods for imaging biological structures, and method for modulating cellular processes using the protein fusion constructs are also provided.

Lagarias, John Clark↗

NASA NTRSDate not supplied

GL4U: Using Space Biology Omics Data to Provide Bioinformatics Training for Students and Educators

NASA’s GeneLab project provides researchers open access to space-relevant multi-omics data via the Open Science Data Repository (OSDR) that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct (training students) and indirect (training educators) approaches. The GL4U pilot programs were conducted in June 2021 (direct training) and 2022 (indirect training). During the pilots, students and educators at Historically Black Colleges and Universities (HBCUs) and Minority Serving Institutions (MSIs) participated in a week-long (direct training) or two-week-long (indirect training) bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze space biology RNA sequencing data from OSDR. During the educator pilot, participants received materials, training, and the necessary compute resources to enable them to run the bootcamp at their home institutions, thereby extending the reach of this initiative. In July 2023, GeneLab is partnering with JPL to expand GL4U to include amplicon sequencing (Amp-Seq) analysis training. During the GL4U Amp-Seq bootcamp, student and educator participants will receive training on how to analyze and interpret Amp-Seq data using the NASA GeneLab data processing pipeline. All bootcamp material, including instructions for requesting compute resources, will be made publicly available on GitHub for educators to teach the GL4U content in subsequent semesters. GL4U provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. We present results from pre- and post-training surveys completed by all participants of the Amp-Seq bootcamp.

Amanda M Saravia-Butler↗

DOE OSTI2025

Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors

Microbial nitrification of fertilizers represents is a significant global source of greenhouse gas emissions. This process increases emissions, fosters toxic algal blooms, and raises crop production costs. Some plants naturally release biological nitrification inhibitors to suppress ammonium-oxidizing microbes and reduce nitrification. Engineering nitrification inhibitor production into food and bioenergy crops via synthetic biology offers a promising mitigation strategy, but its success depends on addressing gaps in our understanding of inhibitor degradation in soil. This study begins to fill this gap by identifying a previously unknown microbial pathway for degrading phenylpropanoid methyl esters, a key class of aromatic nitrification inhibitors. Using transcriptomics and high-throughput functional genomics, we discovered genes essential for phenylpropanoid methyl ester degradation. Genetic and biochemical analyses revealed two novel enzymes, including a newly identified phenylpropanoid methyl esterase, that direct phenylpropanoid methyl esters into known metabolic pathways. Importantly, transferring these genes into bacteria capable of metabolizing other phenylpropanoids enabled them to use the methyl esters as a carbon source. This work provides critical insights into microbial nitrification inhibitor degradation, a poorly understood element of the nitrification cycle.

Genetic Engineering↗

NASA NTRS2006

Conducting Closed Habitation Experiments: Experience from the Lunar Mars Life Support Test Project

The Lunar-Mars Life Support Test Project (LMLSTP) was conducted from 1995 through 1997 at the National Aeronautics and Space Administration s (NASA) Johnson Space Center (JSC) to demonstrate increasingly longer duration operation of integrated, closed-loop life support systems that employed biological and physicochemical techniques for water recycling, waste processing, air revitalization, thermal control, and food production. An analog environment for long-duration human space travel, the conditions of isolation and confinement also enabled studies of human factors, medical sciences (both physiology and psychology) and crew training. Four tests were conducted, Phases I, II, IIa and III, with durations of 15, 30, 60 and 91 days, respectively. The first phase focused on biological air regeneration, using wheat to generate enough oxygen for one experimental subject. The systems demonstrated in the later phases were increasingly complex and interdependent, and provided life support for four crew members. The tests were conducted using two human-rated, atmospherically-closed test chambers, the Variable Pressure Growth Chamber (VPGC) and the Integrated Life Support Systems Test Facility (ILSSTF). Systems included test articles (the life support hardware under evaluation), human accommodations (living quarters, kitchen, exercise equipment, etc.) and facility systems (emergency matrix system, power, cooling, etc.). The test team was managed by a lead engineer and a test director, and included test article engineers responsible for specific systems, subsystems or test articles, test conductors, facility engineers, chamber operators and engineering technicians, medical and safety officers, and science experimenters. A crew selection committee, comprised of psychologists, engineers and managers involved in the test, evaluated male and female volunteers who applied to be test subjects. Selection was based on the skills mix anticipated for each particular test, and utilized information from psychological and medical testing, data on the knowledge, experience and skills of the applicants, and team building exercises. The design, development, buildup and operation of test hardware and documentation followed the established NASA processes and requirements for test buildup and operation.

Barta, Daniel J.↗

NASA NTRS2004

Conducting Closed Habitation Experiments: Experience from the Lunar Mars Life Support Test Project

The Lunar-Mars Life Support Test Project (LMLSTP) was conducted from 1995 through 1997 at the National Aeronautics and Space Administration s (NASA) Johnson Space Center (JSC) to demonstrate increasingly longer duration operation of integrated, closed-loop life support systems that employed biological and physicochemical techniques for water recycling, waste processing, air revitalization, thermal control, and food production. An analog environment for long-duration human space travel, the conditions of isolation and confinement also enabled studies of human factors, medical sciences (both physiology and psychology) and crew training. Four tests were conducted, Phases I, II, IIa and III, with durations of 15, 30,60 and 91 days, respectively. The first phase focused on biological air regeneration, using wheat to generate enough oxygen for one experimental subject. The systems demonstrated in the later phases were increasingly complex and interdependent, and provided life support for four crew members. The tests were conducted using two human-rated, atmospherically-closed test chambers, the Variable Pressure Growth Chamber (VPGC) and the Integrated Life Support Systems Test Facility (ILSSTF). Systems included test articles (the life support hardware under evaluation), human accommodations (living quarters, kitchen, exercise equipment, etc.) and facility systems (emergency matrix system, power, cooling, etc.). The test team was managed by a lead engineer and a test director, and included test article engineers responsible for specific systems, subsystems or test articles, test conductors, facility engineers, chamber operators and engineering technicians, medical and safety officers, and science experimenters. A crew selection committee, comprised of psychologists, engineers and managers involved in the test, evaluated male and female volunteers who applied to be test subjects. Selection was based on the skills mix anticipated for each particular test, and utilized information from psychological and medical testing, data on the knowledge, experience and skills of the applicants, and team building exercises. The design, development, buildup and operation of test hardware and documentation followed the established NASA processes and requirements for test buildup and operation.

Barta, Daniel J.↗

DOE OSTI2024

Biological Upcycling of Plastics Waste

Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non–polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2003

Integrated Optoelectronics for Parallel Microbioanalysis

Miniature, relatively inexpensive microbioanalytical systems ("laboratory-on-achip" devices) have been proposed for the detection of hazardous microbes and toxic chemicals. Each system of this type would include optoelectronic sensors and sensor-output-processing circuitry that would simultaneously look for the optical change, fluorescence, delayed fluorescence, or phosphorescence signatures from multiple redundant sites that have interacted with the test biomolecules in order to detect which one(s) was present in a given situation. These systems could be used in a variety of settings that could include doctors offices, hospitals, hazardous-material laboratories, biological-research laboratories, military operations, and chemical-processing plants.

Stirbl, Robert↗

DOE OSTI2017

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Engineering Robust Production Microbes for Large-Scale Cultivation

Systems biology and synthetic biology are increasingly utilized to review and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these methods. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Intracellular effects of atmospheric-pressure plasmas on melanoma cancer cells

Gas discharge plasmas formed at atmospheric pressure and near room temperature have recently been shown as a promising tool for cancer treatment. The mechanism of the plasma action is attributed to generation of reactive oxygen and nitrogen species, electric fields, charges, and photons. The relative importance of different modes of action of atmospheric-pressure plasmas depends on the process parameters and specific treatment objects. Hence, an in-depth understanding of biological mechanisms that underpin plasma-induced death in cancer cells is required to optimise plasma processing conditions. Here, the intracellular factors involved in the observed anti-cancer activity in melanoma Mel007 cells are studied, focusing on the effect of the plasma treatment dose on the expression of tumour suppressor protein TP73. Over-expression of TP73 causes cell growth arrest and/or apoptosis, and hence can potentially be targeted to enhance killing efficacy and selectivity of the plasma treatment. It is shown that the plasma treatment induces dose-dependent up-regulation of TP73 gene expression, resulting in significantly elevated levels of TP73 RNA and protein in plasma-treated melanoma cells. Silencing of TP73 expression by means of RNA interference inhibited the anticancer effects of the plasma, similar to the effect of caspase inhibitor z-VAD or ROS scavenger N-acetyl cysteine. These results confirm the role of TP73 protein in dose-dependent regulation of anticancer activity of atmospheric-pressure plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Probing growth of metal–organic frameworks with X-ray scattering and vibrational spectroscopy

Nucleation and crystallization arising from liquid to solid phase are involved in a multitude of processes in fields ranging from materials science to biology. Controlling the thermodynamics and kinetics of growth is advantageous to help tune the formation of complex morphologies. In this report, we harness wide-angle X-ray scattering and vibrational spectroscopy to elucidate the mechanism for crystallization and growth of the metal–organic framework Co-MOF-74 within microscopic volumes enclosed in a capillary and an attenuated total reflection microchip reactor. The experiments reveal molecular and structural details of the growth processes, while the results of plane wave density functional calculations allow identification of lattice and linker modes in the formed crystals. Synthesis of the metal–organic framework with microscopic volumes leads to monodisperse and micron-sized crystals, in contrast to those typically observed under bulk reaction conditions. Reduction in the volume of reagents within the microchip reactor was found to accelerate the reaction rate. The coupling of spectroscopy with scattering to probe reactions in microscopic volumes promises to be a useful tool in the synthetic chemist's kit to understand chemical bonding and has potential in designing complex materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Saddle point approaches in strong field physics and generation of attosecond pulses

Attoscience is the emerging field that accesses the fastest electronic processes occurring at the atomic and molecular length scales with attosecond (1 as = 10 –18 s) time resolution having wide ranging physical, chemical, material science and biological applications. The quintessential and one of the most fundamental processes in this domain is the generation of phase locked XUV attosecond pulses. The theoretical approach to understand the process incorporates a fully quantum or semi classical or relativistic description of coherent charge dynamics in intense ultrashort electromagnetic fields driving a quantum system (an atom, a molecule, solid band gap materials or surface plasmas). Modelling of such physical and dynamical systems in science and also in many other branches often leads to equations represented in terms of complex multi-dimensional integrals. These integrals can often be solved using the stationary phase approximation, which leads to a series of equations identifying the points in the multi-dimensional space, having most significant contributions in their evaluation. These points are usually indicated as saddle points. The description of the dynamics of quantum mechanical or relativistic systems that results from such an approach enables near to classical physics intuitive perceptions of the processes under investigation. Thus, the saddle point methods are very powerful and valuable general theoretical tools to obtain asymptotic expressions of such solutions and help also to gain physical insights on the underlying phenomena. Such techniques developed in the past have been adapted to study the emission of as pulses by different physical systems and have been widely employed in calculating and estimating the response of matter to intense electromagnetic pulses on ultrafast time scales. Here we provide an extensive disposition of the saddle point approaches unifying their ubiquitous applications within the domain of attoscience valid for simple atomic to more complex condensed matter systems undergoing ultrafast dynamics and present current trends and advancements in the field. In this review we would delineate the methodology, present a synthesis of seminal works and describe the state of the art applications. Finally we also address ultrashort time dynamics of novel materials that have gained much attention recently, namely lower dimensional material systems and micro-plasma systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit

Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Influenza A Virus Infection, Processed Experimental Dataset Catalog

Influenza A virus (IAV) is a high risk biological agent, classified as a Category C priority pathogen (Orthomyxoviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), and is known to cause severe respiratory disease with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus [NCBITAXON:11320] experimental infection study. Host sample types include human lung adenocarcinoma cells ["Calu-3", BTO:0002750] and whole mouse lung [BTO:0000763] tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Biomimetic, Soft-Material Synapse for Neuromorphic Computing: from Device to Network

Neuromorphic computing refers to a variety of brain-inspired computers, devices, and models inspired by the interconnectivity, performance, and energy efficiency of the human brain. Unlike the ubiquitous von Neumann computer architectures with complex processor cores and sequential computation, biological neurons and synapses operate by storing and processing information simultaneously with the capacity of flexible adaptation resulting in massive computational capability with much less power consumption. The search for a synaptic material which can closely imitate bio-synapse has led to an alamethicin-doped, synthetic biomembrane which can emulate key synaptic functions due to generic memristive property enabling learning and computation. This two-terminal, biomolecular memristor, in contrast to its solid-state counterparts, features similar structure, switching mechanism, and ionic transport modality as biological synapses while consuming considerably lower power. In this paper, we outline a methodology for using this biomolecular synapse to build neural networks capable of solving real-world problems. The physical mechanism underlying its volatile memristance is explored followed by the development of a model of this device for circuit simulation. We outline a circuit design technique to integrate this synapse with solid-state neuron circuit for hardware implementation. Based on these results, we develop a high level simulation framework and use a training scheme called Evolutionary Optimization for Neuromorphic System (EONS) to generate networks for solving two problems, namely iris dataset classification and EEG classification task. The small network size and comparable to state-of-the-art accuracy of these preliminary networks show its potential to enhance synaptic functionality in next generation neuromorphic hardware.

Sakib hasan, Md↗

DOE OSTI2017

Grand Challenges for Biological and Environmental Research: Progress and Future Vision. A Report from the Biological and Environmental Research Advisory Committee

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports research focusing on the interconnections between energy production and the living environment. This fundamental research, conducted at universities, DOE national laboratories, and research institutions across the country, explores organisms and ecosystems that can influence the U.S. energy system and advances understanding of the relationships between energy and environment from local to global scales. Research within BER can be categorized into biological systems and Earth and environmental systems. Biological systems research seeks to characterize and predictively understand microbial and plant systems using genomic science, computational analyses, and experimental approaches. Foundational knowledge of the structure and function of these systems underpins the ability to leverage natural processes for energy production, including the sustainable development of biofuels and other bioproducts. Earth and environmental systems research seeks to characterize and predictively understand feedbacks between Earth and energy systems and includes studies on atmospheric physics and chemistry, ecosystem ecology and biogeochemistry, and development and validation of Earth system models extending from regional to global scales. To promote world-class research in these areas, BER supports user facilities that enable observation and measurement of atmospheric, biological, and biogeochemical processes using the latest technologies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing

The accumulation and extrusion of Ca 2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. In order to emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca 2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca 2+ , respectively. Furthermore, the diffusive memristor and its dynamics enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.

36 MATERIALS SCIENCE↗