Search NASA⌕ Search

SEARCH · Search NASA

Results for “Biological databases”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Effects of light on brain and behavior

It is obvious that light entering the eye permits the sensory capacity of vision. The human species is highly dependent on visual perception of the environment and consequently, the scientific study of vision and visual mechanisms is a centuries old endeavor. Relatively new discoveries are now leading to an expanded understanding of the role of light entering the eye in addition to supporting vision, light has various nonvisual biological effects. Over the past thirty years, animal studies have shown that environmental light is the primary stimulus for regulating circadian rhythms, seasonal cycles, and neuroendocrine responses. As with all photobiological phenomena, the wavelength, intensity, timing and duration of a light stimulus is important in determining its regulatory influence on the circadian and neuroendocrine systems. Initially, the effects of light on rhythms and hormones were observed only in sub-human species. Research over the past decade, however, has confirmed that light entering the eyes of humans is a potent stimulus for controlling physiological rhythms. The aim of this paper is to examine three specific nonvisual responses in humans which are mediated by light entering the eye: light-induced melatonin suppression, light therapy for winter depression, and enhancement of nighttime performance. This will serve as a brief introduction to the growing database which demonstrates how light stimuli can influence physiology, mood and behavior in humans. Such information greatly expands our understanding of the human eye and will ultimately change our use of light in the human environment.

Brainard, George C.↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2004

Intelligent Control for the BEES Flyer

This paper describes the effort to provide a preliminary capability analysis and a neural network based adaptive flight control system for the JPL-led BEES aircraft project. The BEES flyer was envisioned to be a small, autonomous platform with sensing and control systems mimicking those of biological systems for the purpose of scientific exploration on the surface of Mars. The platform is physically tightly constrained by the necessity of efficient packing within rockets for the trip to Mars. Given the physical constraints, the system is not an ideal configuration for aerodynamics or stability and control. The objectives of this effort are to evaluate the aerodynamics characteristics of the existing design, to make recommendaaons as to potential improvements and to provide a control system that stabilizes the existing aircraft for nominal flight and damaged conditions. Towards this several questions are raised and analyses are presented to arrive at answers to some of the questions raised. CART3D, a high-fidelity inviscid analysis package for conceptual and preliminary aerodynamic design, was used to compute a parametric set of solutions over the expected flight domain. Stability and control derivatives were extracted from the database and integrated with the neural flight control system. The Integrated Vehicle Modeling Environment (IVME) was also used for estimating aircraft geometric, inertial, and aerodynamic characteristics. A generic neural flight control system is used to provide adaptive control without the requirement for extensive gain scheduling or explicit system identification. The neural flight control system uses reference models to specify desired handling qualities in the roll, pitch, and yaw axes, and incorporates both pre-trained and on-line learning neural networks in the inverse model portion of the controller. Results are presented for the BEES aircraft in the subsonic regime for terrestrial and Martian environments.

Krishnakumar, K.↗
NASA NTRS2018

Biocene 2018 - Welcome to the Period of New Life

Biocene is the period of new life. When our descendants look back at this period in time, they will see evidence, in the geologic and electronic record, of anthropic climate change, growing population, and scarcity of resources. But they will also see the rebirth of human ingenuity as we overcame the challenges that faced us through nature-inspired exploration. The Periodic Table of Life (PeTaL) is a proposed tool and open source framework that uses artificial intelligence to aid in the systematic inquiry of biology for its application to human systems. This presentation defines the PeTaL concept and workflow. Biomimicry, biophysics, biomimetics, bionics and numerous other terms refer to the use of biology and biological principles to inform practices in other disciplines. For the most part, the domain of inquiry in these fields have been confined to extant biological models with the proponents of biomimicry often citing the evolutionary success of extant organisms relative to extinct ones. The primary objective of this paper is to expand the domain of inquiry for human processes that seek to model those that are, were or could be found in nature with examples that relate to the field of aerospace and to spur development of tools that can work together to accelerate the use of artificial intelligence in problem solving. Specifically specialized fields such as paleomimesis, anthropomimesis and physioteleology are proposed in conjunction with artificial evolution. Blockchain technology may be vital in allowing open source design tools such as PeTaL to democratize design and yet protect intellectual property. The overarching philosophy outlined here can be thought of as physiomimetics, a holistic and systematic way of learning from natural history. The backbone of PeTaL integrates an unstructured database with an ontological model consisting of function, morphology, environment, state of matter and ecosystem. Tools include text classification, thesaurus, data visualization, and analysis. Applications of PeTaL include guiding human space exploration, understanding human and geological history, and discovering new or extinct life.

Biocene↗
DOE OSTI2024

Interactive tools for functional annotation of bacterial genomes

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein’s function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein’s function. Ideally, accurate annotations would allow us to predict a bacterium’s capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Improved Spacecraft Materials for Radiation Protection

Methods by which radiation shielding is optimized need to be developed and materials of improved shielding characteristics identified and validated. The galactic cosmic rays (GCR) are very penetrating and the energy absorbed by the astronaut behind the shield is nearly independent of shield composition and even the shield thickness. However, the mix of particles in the transmitted beam changes rapidly with shield material composition and thickness. This results in part from the breakup of the high-energy heavy ions of the GCR which make contributions to biological effects out of proportion to their deposited energy. So the mixture of particles in the radiation field changes with shielding and the control of risk contributions from dominant particle types is critical to reducing the hazard to the astronaut. The risk of biological injury for a given particle type depends on the type of biological effect and is specific to cell or tissue type. Thus, one is faced with choosing materials which may protect a given tissue against a given effect but leave unchanged or even increase the risk of other effects in the same tissue or increase the risks to other adjacent tissues of a different type in the same individual. The optimization of shield composition will then be tied to a specific tissue and risk to that tissue. Such peculiarities arise from the complicated mixture of particles, the nature of their biological response, and the details of their interaction with material constituents. Aside from the understanding of the biological response to specific components, one also needs an accurate understanding of the radiation emerging from the shield material. This latter subject has been a principal element of this project. In the past ten years our understanding of space radiation interactions with materials has changed radically, with a large impact on shield design. For example, the NCRP estimated that only 2 g/sq cm. of aluminum would be required to meet the annual 500 mSv limit for the exposure of the blood forming organs (this limit is strictly for LEO but can be used as a guideline for the Mars mission analysis). The current estimates require aluminum shield thicknesses above 50 g/sq cm., which is impractical. In such a heavily shielded vehicle, the neutrons produced throughout the vehicle also contribute significantly to the exposure and this demands greater care in describing the angular dependence of secondary particle production processes. As such the continued testing of databases and transport procedures in laboratory and spaceflight experiments has continued. This has been the focus of much of the last year's activity and has resulted in improved neutron prediction capability. These new methods have also improved our understanding of the surface environment of Mars. The Mars 2003 NRA HEDS related surface science requirements were driven by the need to validate predictions on the upward flux of neutrons produced in the Martian regolith and bedrock made by the codes developed under this project. The codes used in the surface environment definition are also being used to look at in situ resources for the development of construction material for Martian surface facilities. For example, synthesis of polyimides and polyethylene as binders of regolith for developing basic structural elements has been studied and targets built for accelerator beam testing of radiation shielding properties. Preliminary mechanical tests have also been promising. Improved spacecraft materials have been identified (using the criteria reported by this project at the last conference) as potentially important for future shielding materials. These are liquid hydrogen, hydrogenated nanofibers, liquid methane, LiH, Polyethylene, Polysulfone, and Polyetherimide (in order of decreasing shield performance). Some of the materials are multifunctional and are required for other onboard systems. We are currently preparing software for trade studies with these materials relative to the Mars Reference Mission as required in the project's final year.

Wilson, John W.↗
DOE OSTI2024

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB

ABSTRACT Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa . Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli , indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase. IMPORTANCE Stenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa . We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Microbial Contamination in the Spacecraft

Spacecraft and space habitats supporting human exploration contain a diverse population of microorganisms. Microorganisms may threaten human habitation in many ways that directly or indirectly impact the health, safety, or performance of astronauts. The ability to produce and maintain spacecraft and space stations with environments suitable for human habitation has been established over 40 years of human spaceflight. An extensive database of environmental microbiological parameters has been provided for short-term (< 20 days) spaceflight by more than 100 missions aboard the Space Shuttle. The NASA Mir Program provided similar data for long-duration missions. Interestingly, the major bacterial and fungal species found in the Space Shuttle are similar to those encountered in the nearly 15-year-old Mir. Lessons learned from both the US and Russian space programs have been incorporated into the habitability plan for the International Space Station. The focus is on preventive measures developed for spacecraft, cargo, and crews. On-orbit regular housekeeping practices complete with visual inspections are essential, along with microbiological monitoring. Risks associated with extended stays on the Moon or a Mars exploration mission will be much greater than previous experiences because of additional unknown variables. The current knowledge base is insufficient for exploration missions, and research is essential to understand the effects of spaceflight on biological functions and population dynamics of microorganisms in spacecraft.

Pierson, Duane L.↗
NASA NTRS2012

Innovative Technologies for Global Space Exploration

Under the direction of NASA's Exploration Systems Mission Directorate (ESMD), Directorate Integration Office (DIO), The Tauri Group with NASA's Technology Assessment and Integration Team (TAIT) completed several studies and white papers that identify novel technologies for human exploration. These studies provide technical inputs to space exploration roadmaps, identify potential organizations for exploration partnerships, and detail crosscutting technologies that may meet some of NASA's critical needs. These studies are supported by a relational database of more than 400 externally funded technologies relevant to current exploration challenges. The identified technologies can be integrated into existing and developing roadmaps to leverage external resources, thereby reducing the cost of space exploration. This approach to identifying potential spin-in technologies and partnerships could apply to other national space programs, as well as international and multi-government activities. This paper highlights innovative technologies and potential partnerships from economic sectors that historically are less connected to space exploration. It includes breakthrough concepts that could have a significant impact on space exploration and discusses the role of breakthrough concepts in technology planning. Technologies and partnerships are from NASA's Technology Horizons and Technology Frontiers game-changing and breakthrough technology reports as well as the External Government Technology Dataset, briefly described in the paper. The paper highlights example novel technologies that could be spun-in from government and commercial sources, including virtual worlds, synthetic biology, and human augmentation. It will consider how these technologies can impact space exploration and will discuss ongoing activities for planning and preparing them.

Hay, Jason↗
DOE OSTI2024

Transcriptomic Analysis of Arachidonic Acid Pathway Genes Provides Mechanistic Insight into Multi-Organ Inflammatory and Vascular Diseases

Arachidonic acid (AA) metabolites have been associated with several diseases across various organ systems, including the cardiovascular, pulmonary, and renal systems. Lipid mediators generated from AA oxidation have been studied to control macrophages, T-cells, cytokines, and fibroblasts, and regulate inflammatory mediators that induce vascular remodeling and dysfunction. AA is metabolized by cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) to generate anti-inflammatory, pro-inflammatory, and pro-resolutory oxidized lipids. As comorbid states such as diabetes, hypertension, and obesity become more prevalent in cardiovascular disease, studying the expression of AA pathway genes and their association with these diseases can provide unique pathophysiological insights. In addition, the AA pathway of oxidized lipids exhibits diverse functions across different organ systems, where a lipid can be both anti-inflammatory and pro-inflammatory depending on the location of metabolic activity. Therefore, we aimed to characterize the gene expression of these lipid enzymes and receptors throughout multi-organ diseases via a transcriptomic meta-analysis using the Gene Expression Omnibus (GEO) Database. In our study, we found that distinct AA pathways were expressed in various comorbid conditions, especially those with prominent inflammatory risk factors. Comorbidities, such as hypertension, diabetes, and obesity appeared to contribute to elevated expression of pro-inflammatory lipid mediator genes. Our results demonstrate that expression of inflammatory AA pathway genes may potentiate and attenuate disease; therefore, we suggest further exploration of these pathways as therapeutic targets to improve outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Microbial contamination of spacecraft

Spacecraft and space habitats supporting human exploration contain a diverse population of microorganisms. Microorganisms may threaten human habitation in many ways that directly or indirectly impact the health, safety, or performance of astronauts. The ability to produce and maintain spacecraft and space stations with environments suitable for human habitation has been established over 40 years of human space flight. An extensive database of environmental microbiological parameters has been provided for short-term (< 20 days) space flight by more than 100 missions aboard the Space Shuttle. The NASA Mir Program provided similar data for long-duration missions. Interestingly, the major bacterial and fungal species found in the Space Shuttle are similar to those encountered in the nearly 15-year-old Mir. Lessons learned from both the US and Russian space programs have been incorporated into the habitability plan for the International Space Station. The focus is on preventive measures developed for spacecraft, cargo, and crews. On-orbit regular housekeeping practices complete with visual inspections are essential, along with microbiological monitoring. Risks associated with extended stays on the Moon or a Mars exploration mission will be much greater than previous experiences because of additional unknown variables. The current knowledge base is insufficient for exploration missions, and research is essential to understand the effects of space flight on biological functions and population dynamics of microorganisms in spacecraft. Equally important is a better understanding of the immune response and of human-microorganism-environment interactions during long-term space habitation.

Mir Project↗
NASA NTRS1999

Multifractality in human heartbeat dynamics

There is evidence that physiological signals under healthy conditions may have a fractal temporal structure. Here we investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system, the healthy human heartbeat, and show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.

Non-NASA Center↗
NASA NTRS2001

Bio-Optical Measurement and Modeling of the California Current and Polar Oceans

This Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) project contract supports in situ ocean optical observations in the California Current, Southern Ocean, Indian Ocean as well as merger of other in situ data sets we have collected on various global cruises supported by separate grants or contracts. The principal goals of our research are to validate standard or experimental products through detailed bio-optical and biogeochemical measurements, and to combine ocean optical observations with advanced radiative transfer modeling to contribute to satellite vicarious radiometric calibration and advanced algorithm development. In collaboration with major oceanographic ship-based observation programs funded by various agencies (CalCOFI, US JGOFS, NOAA AMLR, INDOEX and Japan/East Sea) our SIMBIOS effort has resulted in data from diverse bio-optical provinces. For these global deployments we generate a high-quality, methodologically consistent, data set encompassing a wide-range of oceanic conditions. Global data collected in recent years have been integrated with our on-going CalCOFI database and have been used to evaluate Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) algorithms and to carry out validation studies. The combined database we have assembled now comprises more than 700 stations and includes observations for the clearest oligotrophic waters, highly eutrophic blooms, red-tides and coastal case two conditions. The data has been used to validate water-leaving radiance estimated with SeaWiFS as well as bio optical algorithms for chlorophyll pigments. The comprehensive data is utilized for development of experimental algorithms (e.g., high-low latitude pigment transition, phytoplankton absorption, and cDOM).

Mitchell, B. Greg↗
DOE OSTI2025

Populus VariantDB v3.2 facilitates CRISPR and functional genomics research

The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2020

GeneLab

GeneLab collects and enables analysis of spaceflight and ground-based spaceflight simulation genomic data, RNA and protein expression, and metabolic profiles. It interfaces with other existing databases containing spaceflight omic data. The 2011 National Research Council (NRC) Decadal Survey on NASA Life and Physical Sciences called for increased opportunities for multi-investigator spaceflight opportunities and greater use of genomic approaches to meet the needs of NASA researchers. To address these recommendations of the NRC Decadal Survey, the Space Life and Physical Sciences Research and Applications Division of NASA's Human Exploration and Operations Mission Directorate has initiated a transition to an Open Science architecture to increase research opportunities, and has developed the GeneLab Platform based on highly leveraged and integrated bioinformatics analytics. GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, visualize high-order data and create collaborative projects using the Collaborative Workspace. Our primary goal is to maximize the utilization of the valuable biological research conducted aboard the International Space Station (ISS) by collecting genomic, transcriptomic, proteomic, and metabolomics data known as “omics”. By providing a portal linking processed data to flight parameters, GeneLab enables exploration of the molecular network responses of terrestrial biology to the space environment. This allows researchers to understand the complex responses of biological systems to the space environment. This technology development activity was transferred from the Human Exploration and Operations Mission Directorate to the Science Mission Directorate Division of Biological and Physical Sciences (BPS) in October 2020.

GeneLab↗
NASA NTRS2016

Curating NASA's Past, Present, and Future Astromaterial Sample Collections

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (hereafter JSC curation) is responsible for curating all of NASA's extraterrestrial samples. JSC presently curates 9 different astromaterials collections in seven different clean-room suites: (1) Apollo Samples (ISO (International Standards Organization) class 6 + 7); (2) Antarctic Meteorites (ISO 6 + 7); (3) Cosmic Dust Particles (ISO 5); (4) Microparticle Impact Collection (ISO 7; formerly called Space-Exposed Hardware); (5) Genesis Solar Wind Atoms (ISO 4); (6) Stardust Comet Particles (ISO 5); (7) Stardust Interstellar Particles (ISO 5); (8) Hayabusa Asteroid Particles (ISO 5); (9) OSIRIS-REx Spacecraft Coupons and Witness Plates (ISO 7). Additional cleanrooms are currently being planned to house samples from two new collections, Hayabusa 2 (2021) and OSIRIS-REx (2023). In addition to the labs that house the samples, we maintain a wide variety of infra-structure facilities required to support the clean rooms: HEPA-filtered air-handling systems, ultrapure dry gaseous nitrogen systems, an ultrapure water system, and cleaning facilities to provide clean tools and equipment for the labs. We also have sample preparation facilities for making thin sections, microtome sections, and even focused ion-beam sections. We routinely monitor the cleanliness of our clean rooms and infrastructure systems, including measurements of inorganic or organic contamination, weekly airborne particle counts, compositional and isotopic monitoring of liquid N2 deliveries, and daily UPW system monitoring. In addition to the physical maintenance of the samples, we track within our databases the current and ever changing characteristics (weight, location, etc.) of more than 250,000 individually numbered samples across our various collections, as well as more than 100,000 images, and countless "analog" records that record the sample processing records of each individual sample. JSC Curation is co-located with JSC's Astromaterials Research Office, which houses a world-class suite of analytical instrumentation and scientists. We leverage these labs and personnel to better curate the samples. Part of the cu-ration process is planning for the future, and we refer to these planning efforts as "advanced curation". Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envi-sioned by NASA exploration goals. We are (and have been) planning for future cu-ration, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, and curation of organically- and biologically-sensitive samples.

Zeigler, R. A.↗
DOE OSTI2025

GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics

Data package for Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the below citations for the data packages and associated manuscript. Please cite as: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics. [Data Set] PNNL DataHub. doi: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. MSV000097435: GLBRC soil yearlong incubation 13C-SIP-Lipidomics [Data Set] MassIVE. doi:10.25345/C57659T3K Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon. In Prep This data package consists of compound-specific 13C SIP-lipidomics data from a yearlong tracer incubation experiment designed to investigate microbial lipid persistence in switchgrass bioenergy crop soils. In order to explore how lipid structure may modulate the persistence of C in soil lipids, we leveraged soils from two sites (Michigan - sandy texture, Wisconsin - silty texture) operated by the U.S. Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC). These sites had comparable climates, identical management practices, but contrasting soil textures, allowing us to assess the variability of lipid accrual or degradation in soils as well as provide insight regarding the degree to which edaphic properties may regulate the retention of soil lipids. Untargeted lipidomics analyses were performed to identify 13C-labeled lipids in the soil microbiome after long-term incubation. Soils were supplemented with 100 micrograms glucose per gram dry soil (99 atom % 13C or natural abundance for paired control) and incubated; samples were collected two months and one year after glucose addition. Lipid extracts (MPLEx) were analyzed by LC-MS/MS and identified using LIQUID. Calculation of isotopic enrichment of lipids was performed by targeted approach using TarMet to quantify lipid isotopologues and IsoCorrectoR to correct for natural abundance isotopes. Contents: Data package contents reported here are the first version and contain downstream analysis files for the raw LC-MS mass spectrometry files (.mzXML) deposited at the MassIVE database repository under accession MSV000097435 (80 experimental runs; 5.85 GB) | MassIVE DOI: 10.25345/C57659T3K. Support files include the additional data download 'Read Me' file containing data descriptor information. Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. Data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. Available Data Downloads (0.3 GB): "GLBRC soil yearlong incubation 13C-SIP-Lipidomics_readme.txt" - 'Read Me' data package content file (txt) "GLBRC_DataPackage_analysis files" - Data processing files (Rmd) and saved intermediate data processing outputs (rds, csv, xlsx) "GLBRC_13C_lipidomics_dataset.xlsx" - processed data in tabular format (xlsx) Linked Software: LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462 Lipid Mini-On Software Tools | 10.5281/zenodo.1492803 pmartR Omics Statistical Software | 10.5281/zenodo.6108667 xcms (v4.3.3) TarMet (v1.1.1) IsoCorrectoR (1.24.0) Funding Acknowledgments: This research was supported by an Early Career Research Program award funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (OBER) Genomic Science program under FWP 68292, FWP 07880 and EMSL Exploratory Research Project 51095. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by OBER and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830.

Rempfert, Kaitlin R [Pacific Northwest National La↗