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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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All sources NASA NTRS DOE OSTI

NASA NTRS1994

The 1992-1993 NASA Space Biology Accomplishments

This report consists of individual technical summaries of research projects of NASA's Space Biology Program, for research conducted during the calendar years of 1992 and 1993. This program includes both plant and animal research, and is dedicated to understanding the role of gravity and the effects of microgravity on biological processes; determining the effects of the interaction of gravity and other environmental factors on biological systems; and using the microgravity of the space environment as a tool to advance fundamental scientific knowledge in the biological sciences to improve the quality of life on Earth and contribute to NASA's goal of manned exploration of space. The summaries for each project include a description of the research, a list of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

Halstead, Thora W.↗

DOE OSTI2016

Roles of Rack1 Proteins in Fungal Pathogenesis

Pathogenic fungi cause diseases on various organisms. Despite their differences in life cycles, fungal pathogens use well-conserved proteins and pathways to regulate developmental and infection processes. In this review, we focus on Rack1, a multifaceted scaffolding protein involved in various biological processes. Rack1 is well conserved in eukaryotes and plays important roles in fungi, though limited studies have been conducted. To accelerate the study of Rack1 proteins in fungi, we review the functions of Rack1 proteins in model and pathogenic fungi and summarize recent progress on how Rack1 proteins are involved in fungal pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Mass Spectrometry Sample Submission Portal

Each step in the scientific process generates contextual information about the data that is important to consider when performing data integration, developing models of biological process, or training AI models. We will develop a flexible, template-driven tool that will log biological samples, capture metadata about those samples, and track the type(s) of analysis being performed by researchers providing samples for analysis by mass spectrometry.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

The evolution of analytical techniques for multiplex analysis of protein biomarkers

Introduction: The landscape of biomarker development has evolved with advanced analytical technologies, particularly affinity- and mass spectrometry-based techniques. These advancements have deepened our understanding of disease mechanisms, enabling the development of precise diagnostic tools and personalized medicine. Protein biomarkers, which play pivotal roles in biological processes, have become invaluable in diagnosing and monitoring diseases, aided by their presence in various biological samples and the availability of established detection methods. Areas covered: This review covers the role of protein biomarkers in clinical practice, the development and dimensionality of protein biomarkers, advancements in detection technologies, a comparison of these technologies, and future directions in biomarker discovery and disease mechanism elucidation. Expert opinion: Advances in biomarker technologies have the potential to transform diagnostics and personalized treatment but face challenges such as high costs and technical complexity. Enhancing reproducibility and integrating multi-omics approaches may offer better insights. In conclusion, the field should evolve toward high-throughput, automated methods, continuously adapting research, and clinical practices.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Investigation of protein quaternary structure via stoichiometry and symmetry information

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Effects of small marine energy deployments on oceanographic systems

The placement and operation of marine energy deployments in the ocean have the potential to change flow patterns, decrease wave heights, and/or remove energy from the oceanographic system. Changes in oceanographic systems resulting from harvesting marine energy, particularly tidal and wave energy, may be of concern. These changes include alterations in nearfield and farfield physical processes, as well as potential secondary environmental effects such as changes in sediment transport patterns, biological processes, or coastal erosion. Knowledge of changes in oceanographic systems associated with marine energy is primarily available from numerical modeling studies, informed by some laboratory tests and very few field measurements. A literature review was conducted using the Tethys knowledge base and other online sources, building on conclusions from the Ocean Energy Systems-Environmental State of the Science report. Potential changes in oceanographic systems that may be caused by marine energy differ between tidal and wave devices because of different extraction mechanisms and siting locations. Numerical models show that tidal extraction on the order of hundreds of megawatts or with significant channel blockage is required to create changes in oceanographic processes that exceed natural variability. Effects from wave energy extraction in arrays are localized and dependent on array spacing and proximity to the shore. Here the available evidence supports the conclusion that the risk of significant environmental effects from such changes could be retired (i.e., less investigation required for every project) for small deployments—those representative of the state of the industry in 2021. Determining changes in oceanographic systems to be low risk for small deployments can thereby streamline environmental consenting by reducing monitoring needs at this early stage in the industry.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2000

Ceratopteris richardii: a productive model for revealing secrets of signaling and development

Ceratopteris richardii is an aquatic fern grown in tropical and subtropical regions of the world. It is proven to be a productive model system for studies in the genetics, biochemistry, and cell biology of basic biologic processes that occur in early gametophytic development. It provides several advantages to biologists, especially those interested in gravitational biology, polarity development, and in the genetics of sexual development. It is easy to culture, has a relatively short life cycle, and offers an array of attractive features that facilitate genetic studies. The germination and early development of large populations of genetically identical spores are easy to synchronize, and both the direction of polarity development and cell-level gravity responses can be measured and readily manipulated within the first 24 h of spore development. Although there is no reliable transformation system available yet in Ceratopteris, recent studies suggest that the technique of RNA interference can be used to block translation of specific genes in a related fern, Marsilea, and current studies will soon reveal the applicability of this approach, as well as of other transformation approaches, in Ceratopteris. A recently completed expressed sequence tag (EST) sequencing project makes available the partial sequence of more than 2000 cDNAs, representing a significant percentage of the genes being expressed during the first 24 h of spore germination, when many developmentally interesting processes are occurring. A microarray of these ESTs is being constructed, so especially for those scientists interested in basic cellular phenomena that occur early in spore germination, the availability of the ESTs and of the microarray will make Ceratopteris an even more attractive model system.

NASA Discipline Plant Biology↗

DOE OSTI2018

Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties

Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li + , Na + , K + , Cs + , Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg 2+ . As a result, using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

An overview: recycling nutrients from crop residues for space applications

Without some form of regenerative life support system, long duration space habitation or travel will be limited severely by the prohibitive costs of resupplying air, water, and food from Earth. Components under consideration for inclusion in a regenerative life support system are based on either physicochemical or biological processes. Physicochemical systems would use filtration and elemental phase changes to convert waste materials into usable products, while biological systems would use higher plants and bioreactors to supply crew needs. Neither a purely biological nor strictly a physicochemical approach can supply all crew needs, thus, the best each approach can offer will be combined into a hybrid regenerative life support system. Researchers at Kennedy Space Center (KSC) Advanced Life Support Breadboard Project have taken the lead on bioregenerative aspects of space life support. The major focus has been on utilization of higher plants for production of food, oxygen, and clean water. However, a key to any regenerative life support system is recycling and recovery of resources (wastes). In keeping with the emphasis at KSC on bioregenerative systems and with the focus on plants, this paper focuses on research with biologically-based options for resource recovery from inedible crop residues.

Biomass↗

NASA NTRS2000

Low Pressure Greenhouse Concepts for Mars

A project was initiated to begin testing some environmental limits for managing plant growth systems. These limits will help determine some of the concepts for building plant enclosures for use on Mars. In particular, this study focuses on the effects of reduced atmospheric pressures. Structural design is considered as it relates to the biological processes that would occur within that structure. The design must be closely tied to the functionality of the biological system and has a few primary concerns that need to be tested to resolve the question as to the path of the design. Early tests indicate that plants can survive and grow at low (greater than 76 mb) pressure.

Fowler, Philip A.↗

NASA NTRSDate not supplied

Transcriptomic Analysis of Irradiated Mouse Retina Following Readaptation

Rodent models are used as analogs for studying the effects of spaceflight. NASA GeneLab provides access to relevant omics datasets generated from spaceflight and ground-based experiments allowing for additional retrospective analysis. In this study, we used GeneLab’s GLDS-203, a dataset generated by researchers at Loma Linda University to study the impact of prolonged unloading and/or low-dose radiation on mouse retina. We analyzed transcriptomics data from retina of mice irradiated with gamma-rays for 21 days followed by 7 days, 1 month, or 4 months of readaptation. We obtained raw gene counts from GeneLab and performed differential gene expression analysis after data normalization. For each of the three timepoints, we performed differential expression analysis to compare transcriptional profiles for retina from irradiated vs. non-irradiated (controls) mice, all exposed to gravity. We observed the highest number of differentially expressed genes at 7 days, followed by 1 month and 4 months. Enrichment analysis showed top pathways (adjusted p-value < 0.05) were related to transport along microtubule and photoreceptor cell development in the 7-day readaptation group. Fewer significantly enriched pathways were observed for the 1-month group and included mRNA metabolic processes and neuron differentiation. No significantly enriched pathways were found in the 4-month group. The Gene Ontology biological processes common between the 7 days and 1-month groups include visual perception, synapse organization, and perception of light stimulus. This analysis is part of a larger effort to characterize the molecular mechanisms involved in retinal readaptation following radiation exposure. Future analyses will include other related retina datasets in GeneLab repository to assess whether gene expression patterns are consistent across different study cohorts.

Prachi Kothiyal↗

DOE OSTI2024

Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings

As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1990

A robotic return to the moon

The autonomous lunar precursor mission presently proposed for low cost manned revisits to the lunar surface, designated 'Lunar Oasis by Automation and Robotics', employs two self-similar robotic vehicles, and three experimental 'biovolumes' which are directly derived from the lunar landers that are initially entrusted with fulfilling mission hardware-delivery requirements. The two vehicles would support the experimental biovolumes by returning resources for use in physicochemical or biological processing. Delivered resources would be combined with those in situ to furnish reconfigured biovolumes with the capabilities for autonomous biological growth and wastes-reprocessing demonstrations.

Luttges, Marvin W.↗

NASA NTRS2015

Prototype Biology-Based Radiation Risk Module Project

Biological effects of space radiation and risk mitigation are strategic knowledge gaps for the Evolvable Mars Campaign. The current epidemiology-based NASA Space Cancer Risk (NSCR) model contains large uncertainties (HAT #6.5a) due to lack of information on the radiobiology of galactic cosmic rays (GCR) and lack of human data. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. Our proposed study will compare DNA damage, histological, and cell kinetic parameters after irradiation in normal 2D human cells versus 3D tissue models, and it will use a multi-scale computational model (CHASTE) to investigate various biological processes that may contribute to carcinogenesis, including radiation-induced cellular signaling pathways. This cross-disciplinary work, with biological validation of an evolvable mathematical computational model, will help reduce uncertainties within NSCR and aid risk mitigation for radiation-induced carcinogenesis.

Terrier, Douglas↗

DOE OSTI2024

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

ABSTRACT Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS − ). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS 2 ). Recently, paradigm-shifting studies indicate that Fe and S in FeS 2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS 2 , as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS 2 , Fe(II)/HS − , or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS − , either as a component of the growth medium [Fe(II)/HS − ] or generated through reduction of FeS 2 , were likely a major factor underpinning these phenotypic differences. IMPORTANCE The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Membrane Carbonation for 100% Efficient Delivery of Industrial CO 2 Gases

Industrial processes generate about one quarter of all greenhouse gases emissions in the US, about 80% of which is carbon dioxide (CO 2 ). Biological processes are one of the largest natural sinks for atmospheric CO 2 , but the rate of capture is limited by the low concentration in air (~0.04%). Industrial emissions have significantly higher CO 2 concentrations, ranging from 5–80% CO 2 , which can significantly increase the rate of biological CO 2 capture, including many-fold improvements for cultivating microalgae to produce food, fertilizer, and renewable fuel. However, traditional methods for delivering CO 2 to microalgae using bubbling is < 40% efficient, leading to significant residual CO 2 emissions and increased cost. This project developed the Membrane Carbonation (MC) technology to significantly improve the CO 2 delivery efficiency to microalgae from power plant flue gas, wastewater treatment plant anaerobic digesters biogas (Figure 1), and other CO 2 -containing industrial sources.

09 BIOMASS FUELS↗

DOE OSTI2017

The S.An.A.® concept: Semi-aerobic, Anaerobic, Aerated bioreactor landfill

Highlights: • Sustainable Hybrid bioreactor landfill lab-scale application. • Semi-aerobic, Anaerobic, Aerated (S.An.A.®) concept. • Enhancement of methane production and biochemical processes. • Aeration and flushing for reaching Final Storage Quality. - Abstract: Hybrid Bioreactor Landfills are designed to enhance and speed up biological processes, aiming at reducing the duration of post operational phase until landfill completion. S.An.A.®(Semi-aerobic, Anaerobic, Aerated) concept consists in a Hybrid Bioreactor featuring a first semi-aerobic phase to enhance the methane production occurring in the following anaerobic step and a forced aeration for the abatement of the residual emissions. At the end of the last step, semi-aerobic conditions are restored and flushing applied for leaching residual non-biodegradable compounds. Results of the application of S.An.A.® concept to a lab scale bioreactor system showed that pre-aeration was effective in controlling the concentration of VFA, increasing pH and stimulating methane production during anaerobic phase; in particular with intermittent airflow the methane potential was 50% higher respect to control reactors. Forced aeration reduced organic compounds and nitrogen concentration in leachate of an order of magnitude, better performing in low airflow reactors. S.An.A.® Hybrid bioreactors proved to be an efficient system both for increasing methane production and reaching landfill completion in shorter time, suggesting that with proper landfill management, the duration of post-closure care might be reduced by 25–35%.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗