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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Initial analysis of “stone” size Ryugu samples: current status

As a part of the initial analysis of the Ryugu samples, we perform a variety of analyses of millimeter-sized "stones". Our goals are to elucidate the entire formation process of C-type asteroid Ryugu from the viewpoint of petrology and mineralogy ande obtain necessary information by sample analysis, and then simulate the formation of Ryugu based on the evidencef obtained rom sample analysis. Eighteen stones (8 from Room A and 10 from Room C) were received from the ISAS curation facility on June 1, 2021, and brought into a fully nitrogen-displaced glove box at Tohoku University. At the same time, we also received the powder samples from Room A and Room C. To completely block the atmosphere from leaking into the container, all samples were put in the sample transport containers prepared by ISAS, transferred from the main chamber to the glovebox at ISAS, and then all containers were completely sealed in plastic bags with moisture and oxygen absorbers. No moisture or oxygen was detected when the bags were opened in the glove box at Tohoku University, so it was confirmed that there was no exposure to the atmosphere during transport. To date, a number of analyses have been carried out successfully and almost on schedule. The analysis started with the measurement of reflectance spectra, which are sensitive to atmospheric oxidation, hydroxylation, and adsorbed water. The visible, near-infrared, and mid-infrared reflectance spectra were measured while the samples were kept airtight. The spectra of powder samples and stone samples (as aggregates and as single stone) were successfully obtained. A major feature of the stone team's analysis is the use of synchrotron radiation facilities around the world. Since this analysis is non-destructive, stone samples whose reflectance spectra were measured were sent to KEK, SPring-8, ESRF (France), SOLEIL (France), DESY (Germany), and APS (USA). Using these synchrotron radiation facilities, high spatial resolution and sensitivity XRD, STXM, XANES, CT [1], IR-CT, FT-IR [2, 3], XRF, and Mössbauer analyses were performed. Most of the analyses were carried out under air-tight conditions on the stone samples and the particulates separated from the stone samples. These analyses allowed us to determine the three-dimensional distribution of minerals and elements, redox state, density and porosity of the stone samples. Furthermore, as a characteristic analysis of the stone team, light elemental analysis using negative Muon was performed at the MLF facility of J-PARC with an exceptionally long allocation of machine time. This is the only non-destructive method to measure the concentration of light elements in the whole (not the surface) of stone samples. Because the characteristic X-rays produced by muon irradiation are much higher in energy than the fluorescent X-rays produced by X-ray irradiation, there is little effect of self-absorption by the sample, and therefore, the concentration of light elements such as carbon, oxygen, and Na in the entire "stone" sample can be determined. Some stone samples are currently being measured for heat and strength physical properties in order to understand the physical properties of asteroid Ryugu. The data obtained from these measurements are useful for interpreting the remote-sensing data data taken from the surface layer of the asteroid Ryugu [4-7]. It is also important for understanding the behavior of the Ryugu material during impact events. The surfaces of many stone samples were observed by electron microscopy and other techniques, especially on natural “flat” surfaces formed on 5 stomes. As a result, characteristric mineral aggregates formed by the reactions with water and characteiristic impact features were observed on some of the samples. Based on the observations of surfaces and the synchrotron measurements of the whole stones, important objects such as characteristic structures and specific crystal aggregates for understanding the formation history of the asteroid were identified, and these parts were separated from the stone samples using an Xe beam (pFIB) and analyzed by various methods including transmission electron microscopy and synchrotron radiation analysis. Many stone samples, from which important objects have been separated, are embedded in epoxy resin and cut to produce many polished sections. Electron microscopy and spectroscopic measurements of the polished surfaces are being carried out to reveal the detailed mineralogical properties and elemental distribution inside the stone samples. In the fall, machine time for synchrotron radiation will begin, and we plan to analyze single crystals and characteristic objects separated from the stone samples.

Tomoki Nakamura↗
DOE OSTI2019

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes as a public database for diagnostic purposes and demonstrate its utility on the example of two use cases. We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests. The use of FDA-ARGOS as an in silico target sequence comparator tool combined with representative clinical testing could reduce the burden for completing ID-NGS clinical trials

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

The distribution, diversity and function of predominant Thermoproteales in high‐temperature environments of Yellowstone National Park

Summary High‐temperature environments (> 70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of different Thermoproteales genera across geochemically distinct geothermal habitats of Yellowstone National Park, and to identify key functional attributes of major genera that correlate with environmental parameters. Curated sequence assemblies belonging to five genera were characterized in replicate samples of 11 high‐temperature communities ranging in pH from 3 to 9. Thermocladium , Vulcanisaeta and Caldivirga spp. were the primary Thermoproteales populations present in low pH (pH < 5) habitats, whereas Thermoproteus populations were found in mildly‐acidic (pH 5–6) sulfur sediments, and Pyrobaculum populations were confined to higher pH (pH > 6) sulfur sediments and/or filamentous ‘streamer’ communities. Metabolic reconstruction and comparative genomics among assemblies show that these populations are primarily chemoorganotrophs that utilize different electron acceptors depending on geochemical conditions. The presence of potential CO 2 fixation pathways in some Thermoproteales populations appears to be linked with NiFe hydrogenases, which combined with high levels of H 2 in many sulfidic systems, may provide the energy required to fix inorganic C.

Jay, Zackary J.↗
DOE OSTI2022

The Gaia EDR3 view of Johnson-Kron-Cousins standard stars: the curated Landolt and Stetson collections

In the era of large surveys and space missions, it is necessary to rely on large samples of well-characterized stars for inter-calibrating and comparing measurements from different surveys and catalogues. Among the most employed photometric systems, the Johnson-Kron-Cousins has been used for decades and for a large amount of important datasets. Our goal is to profit from the Gaia EDR3 data, Gaia official cross-match algorithm, and Gaia -derived literature catalogues, to provide a well-characterized and clean sample of secondary standards in the Johnson-Kron-Cousins system, as well as a set of transformations between the main photometric systems and the Johnson-Kron-Cousins one. Using Gaia as a reference, as well as data from reddening maps, spectroscopic surveys, and variable stars monitoring surveys, we curated and characterized the widely used Landolt and Stetson collections of more than 200 000 secondary standards, employing classical as well as machine learning techniques. In particular, our atmospheric parameters agree significantly better with spectroscopic ones, compared to other machine learning catalogues. We also cross-matched the curated collections with the major photometric surveys to provide a comprehensive set of reliable measurements in the most widely adopted photometric systems. We provide a curated catalogue of secondary standards in the Johnson-Kron-Cousins system that are well-measured and as free as possible from variable and multiple sources. We characterize the collection in terms of astrophysical parameters, distance, reddening, and radial velocity. We provide a table with the magnitudes of the secondary standards in the most widely used photometric systems (ugriz, grizy, Gaia , HIPPARCOS, Tycho , 2MASS). We finally provide a set of 167 polynomial transformations, valid for dwarfs and giants, metal-poor and metal-rich stars, to transform UBVRI magnitudes in the above photometric systems and vice-versa.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2013

Reducing Organic Contamination in NASA JSC Astromaterial Curation Facility

Future robotic and human spaceflight missions to the Moon, Mars, asteroids and comets will require handling and storing astromaterial samples with minimal inorganic and organic contamination to preserve the scientific integrity of each sample. Much was learned from the rigorous attempts to minimize and monitor organic contamination during Apollo, but it was not adequate for current analytical requirements; thus [1]. OSIRIS-REx, Hayabusa-2, and future Mars sample return will require better protocols for reducing organic contamination. Future isolation con-tainment systems for astromaterials, possibly nitrogen enriched gloveboxes, must be able to reduce organic and inorganic cross-contamination. In 2012, a baseline study established the current state of organic cleanliness in gloveboxes used by NASA JSC astromaterials curation labs that could be used as a benchmark for future mission designs [2, 3]. After standard ultra-pure water (UPW) cleaning, the majority of organic contaminates found were hydrocarbons, plasticizers, silicones, and solvents. Hydro-carbons loads (> C7) ranged from 1.9 to 11.8 ng/cm2 for TD-GC-MS wafer exposure analyses and 5.0 to 19.5 ng/L for TD-GC-MS adsorbent tube exposure. Plasticizers included < 0.6 ng/cm2 of DBP, DEP, TXIB, and DIBP. Silicones included < 0.5 ng/cm2 of cyclo(Me2SiO)x (x = 6, 8, 9, 10) and siloxane. Solvents included < 1.0 ng/cm2 of 2-cyclohexen-1-one, 3,5,5-trimethyl- (Isopho-rone), N-formylpiperidine, and 2-(2-butoxyethoxy) ethanol. In addition, DBF, rubber/polymer additive was found at < 0.2 ng/cm2 and caprolactam, nylon-6 at < 0.6 ng/cm2. Reducing Organics: The Apollo program was the last sam-ple return mission to place high-level organic requirements and biological containment protocols on a curation facility. The high vacuum complex F-201 glovebox in the Lunar Receiving Labora-tory used ethyl alcohol (190 proof), 3:1 benzene/methanol (nano grade solution), and heat sterilization at 130degC for 48 hours to reduce organic contamination. In addition, both heat sterilization and peracetic acid sterilization were used in the atmospheric de-contamination (R) cabinets. Later, Lunar curation gloveboxes were degreased with a pressurized Freon 113 wash. Today, UPW has replaced Freon as the standard cleaning procedure, but does not have the degreasing solvency power of Freon. Future Cleaning Studies: Cleaning experiments are cur-rently being orchestrated to study how to degrease and reduce organics in a JSC curation glovebox lower than the established baseline. Several new chemicals in the industry have replaced traditional degreasing solvents such as Freon and others that are now federally restricted. However, these new suites of chemicals remain untested for lowering organics in curation gloveboxes. 3M's HFE-7100DL and DuPont's Vertrel XF are currently being tested as a replacement for Freon 113 as a degreaser at JSC cura-tion facilities. In addition, the use of UPW as a final rinse is be-ing tested, which presumably can maintain a lower total organic carbon load than the filtered purity of chemical solutions. References: [1] Allton J.H. et al. (2012) LPS XLIII, 2439; [2] Calaway M.

Calaway, M. J.↗
DOE OSTI2019

Experimental Data Curation at Large Instrument Facilities with Open Source Software

The National Synchrotron Light Source II operating at Brookhaven National Laboratory since 2014 for the US Department of Energy is one of the newest and brightest storage-ring synchrotron facility in the world. NSLS-II, like other facilities, provides pre-processing of the raw data and some analysis capabilities to its users. We describe the research collaborations and open source infrastructure developed at large instrument facilities such as NSLS-II for the purpose of curating high value scientific data along the early stages of the data lifecycle. Data acquisition and curation tasks include storing experiment configuration, detector metadata, raw data acquisition with infrastructure that converts proprietary instrument formats to industry standards. In addition, we describe a specific effort for discovering sample information at NSLS-II and tracing the provenance of analysis performed on acquired images. We show that curation tasks must be embedded into software along the data life cycle for effectiveness and ease of use, and that loosely defined collaborations evolve around shared open source tools. Finally we discuss best practices for experimental metadata capture in such facilities, data access and the new challenges of scale and complexity posed by AI-based discovery for the synthesis of new materials.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRSDate not supplied

Ultrapure Water System at JSC for High Purity Cleaning of Flight Hardware, Astromaterial Handling Tools and Solar Wind Samples

Use of Ultrapure Water (UPW) for cleaning of astromaterial sample handling tools and containers was driven by the discontinuation of Freon 113 as a cleaning solvent, due to environmental concerns. Freon 113, recycled using distillation, was very effective at removing organic residues from sample handling hardware. The initial switch to high purity water for astromaterial tool cleaning was modeled after efforts at White Sands Test Facility (WSTF) and current semiconductor UPW production practices in the early 1990s. JSC curation’s first system was comprised of ion exchange polishing cylinders, 55 gallon PVDF-lined storage tank, a few tens of feet of PVDF piping, UV and particle filtration, and this system supported cleaning for lunar, meteorite and Cosmic Dust collectors lab operations. By 2000 a major expansion and upgrade was providing UPW of quality E-1 (ASTM D5127-90) or better at 10 gpm for cleaning of the Genesis solar wind payload for flight, in addition to sample handling tools for other astromaterials. This expansion included a 1000 gallon storage tank and several hundred feet of PVDF piping located in B. 31 and 31N. An extra reverse osmosis process unit was added to incoming water in 2005. Subsequently several major components were replaced, and in anticipation of adding new labs, an enlarged UPW system was designed in 2018 and completed in 2019. This system produces grade E1.1 UPW at 15 gpm in a continuous 1100 ft. loop with 5000 gal. storage tank, supplying 8 laboratories.

Ultrapure water↗
NASA NTRS2018

The OSIRIS-REx Spacecraft and the Touch-and-Go Sample Acquisition Mechanism (TAGSAM)

The Origins, Spectral-Interpretation, Resource-Identification, Security and Regolith- Explorer (OSIRIS-REx) spacecraft supports all aspects of the mission science objectives, from extensive remote sensing at the asteroid Bennu, to sample collection and return to Earth. In general, the success of planetary missions requires the collection, return, and analysis of data, which in turn depends on the successful operation of instruments and the host spacecraft. In the case of OSIRIS-REx, a sample-return mission, the spacecraft must also support the acquisition, safe stowage, and return of the sample. The target asteroid is Bennu, a B-class near-Earth asteroid roughly 500 m diameter. The Lockheed Martin-designed and developed OSIRIS-REx spacecraft draws significant heritage from previous missions and features the Touch-and-Go-Sample-Acquisition-Mechanism, or TAGSAM, to collect sample from the surface of Bennu. Lockheed Martin developed TAGSAM as a novel, simple way to collect samples on planetary bodies. During short contact with the asteroid surface, TAGSAM releases curation-grade nitrogen gas, mobilizing the surface regolith into a collection chamber. The contact surface of TAGSAM includes "contact pads", which are present to collect surface grains that have been subject to space weathering. Extensive 1-g laboratory testing, "reduced-gravity" testing (via parabolic flights on an airplane), and analysis demonstrate that TAGSAM will collect asteroid material in nominal conditions, and a variety of off-nominal conditions, such as the presence of large obstacles under the TAGSAM sampling head, or failure in the sampling gas firing. TAGSAM, and the spacecraft support of the instruments, are central to the success of the mission.

Spacecraft↗
NASA NTRS2024

2023 Cleanroom Monitoring for OSIRIS-REx

OSIRIS-REx is an asteroid sample return mission that delivered asteroid regolith from Bennu to Earth on 9/24/2023 [1]. Cleanroom monitoring of OSIRIS-REx Curation facilities has been ongoing since 2021 when construction of the OSIRIS-REx lab at Johnson Space Center (JSC) was completed [2]. The monitoring continues inside of the OSIRIS-REx lab in Houston. Monitoring was also conducted on a temporary cleanroom constructed inside a hangar at the Utah Test and Training Range (UTTR) to initially receive the Sample Return Capsule (SRC) upon its landing there. The following reports on cleanroom monitoring that has taken place in the months leading up to as well as after OSIRIS-REx return. Monitoring techniques used include particle counts, deployment of Si wafer witness plates (Balazs, Inc.) and Al foil witness plates, gas sampling (Balazs, Inc.) and microbiological monitoring. We collected particle counts at both the lab at JSC as well as the temporary cleanroom at UTTR. Particle counts were taken monthly from six locations in the lab at JSC. Particle counts were taken from seven locations at UTTR in July, August, and September. The UTTR cleanroom particle counts were taken daily in the five days leading to OSIRIS-REx return as well as consistently the day of return (every 2 minutes and 15 seconds 7:21 am- 6:27 pm) from one location inside the cleanroom. The particle counts at UTTR consistently stayed well within the ranges of its required ISO 7 equivalent classification (352,000 maximum particles/ m3 ≥ 0.5 μm). Most analysis showed that the particle counts were far below ISO 7 requirements (highest measured count was 61,484 particles/ m3 ≥ 0.5 um). but the elevated instances correlated to exterior hangar doors being open. Particle counts were reduced when keeping exterior hangar doors closed. The particle counts at JSC have stayed consistently within their ISO 5 equivalent classification (3,520 maximum particles/ m3 ≥ 0.5 um). In most instances, the counts are much better except in one instance where the count measured 13,381 particles/ m3 ≥ 0.5 um. The high spike in particle counts in the JSC lab correlated with the air handlers being shut down temporarily the previous day. The particle counts taken in the same location quickly reduced and measured 0 when taken a month later with the air handlers on. We deployed 8-inch semiconductor polished Si wafer witness plates for 24-hour periods inside of the OSIRIS-REx Curation lab at JSC (in July, August, September, and November 2023) and the cleanroom at UTTR (July and September 2023) to test for possible organic and inorganic contaminants. We also deployed these wafers inside of the OSIRIS-REx Touch-and-Go sample Acquisition Mechanism (TAGSAM) glovebox (where Bennu sample processing occurs) and desiccator (Bennu sample storage) at JSC in August 2023. These samples were all sent to Balazs for analysis via Thermal Desorption Gas Chromatography Mass Spectroscopy (TD-GC-MS) to quantify organic compounds and vapor phase decomposition inductively coupled plasma mass spectrometry (VPD-ICP-MS) to quantify inorganic contaminants. We collected air samples using an adsorbent tube connected to a pump for six hours (100 mL/minute) inside of both the JSC lab and the UTTR cleanroom. These samples were taken at JSC in July, August, September, November, and December and at UTTR in July and September. Additionally, a sample was taken just outside of the TAGSAM glovebox airlock door in July. These samples were sent to Balazs for analysis of volatile organics in air. Overall, the OSIRIS-REx lab at JSC and cleanroom at UTTR yielded very low organic and inorganic contaminants (similar results to Genesis lab at JSC which is ISO 4 equivalent) except for boron, which is attributed to the borosilicate glass in the fan filter units. We collected monthly surface and air samples inside the JSC lab to monitor potential microbial contamination. We report the recovery rate for each sampling event, which is defined as the number of samples exhibiting bacterial or fungal growth divided by the total number of samples collected. Since the lab was commissioned in 2021 the median recovery rate is 29%. This recovery rate is consistent with other ISO 5 equivalent labs used to curate astromaterials collections. Increases in recovery rate correspond to construction and/or extra activity in the lab. However, increases in recovery rate do not reliably correlate to increases in particle counts, which highlights the need for a dedicated microbial monitoring program for biologically sensitive collections. We sampled the temporary clean room at UTTR in July, August, and September of 2023 to monitor potential microbial contamination. The recovery rate decreased from 80% in August to 29% in September. However, in all instances, the diversity of bacteria and fungi was higher in the UTTR cleanroom than in the JSC lab. We routinely collected more than twenty different organisms from the UTTR cleanroom. In the JSC lab the median diversity is 2 organisms. Based on these results we hypothesize that microbes from UTTR could be transported back to JSC with the Bennu samples. To mitigate this risk, in September of 2023, we implemented additional cleaning procedures in the JSC lab to reduce the bioburden on surfaces that could come into direct contact with hardware used to process Bennu samples. Since adopting these additional cleaning measures, the median recovery rate has decreased to 14%. We did not observe an increase in fungal or bacterial diversity in the lab in the October sampling. We will continue to monitor this trend closely for the next several months. Supported by NASA under Award NNH09ZDA007O and Contract NNM10AA11C.

Rachel Comstock Funk↗
NASA NTRSDate not supplied

MSR Science Planning Group 2 (MSPG2): Science & Curation Considerations for Time Sensitive Measurements That Should be Performed in Containment

The Perseverance rover is currently collecting samples on the martian surface for potential return to Earth and planning is underway to develop facilities to study these samples. Perseverance will collect up to 38 samples that will be sealed in TiN tubes. As long as the tubes remain sealed the samples will be metastable. However, as soon as a tube is opened, or headspace gas is extracted these samples will begin to re-equilibrate with their new surroundings. The MSPG2 time-sensitive science sub-group attempted to quantify the rates at which alteration is likely to occur assuming the samples are opened and stored in a nitrogen atmosphere at room temperature. The group also recommended ~20 instruments for inclusion in a sample receiving facility to allow the time sensitive properties of these samples to be measured before they are irreversibly altered.

Aaron B Regberg↗
NASA NTRS2014

GeoLab: A Geological Workstation for Future Missions

The GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance theThe GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance the early scientific returns from future missions and ensure that the best samples are selected for Earth return. The facility was also designed to foster the development of instrument technology. Since 2009, when GeoLab design and construction began, the GeoLab team [a group of scientists from the Astromaterials Acquisition and Curation Office within the Astromaterials Research and Exploration Science (ARES) Directorate at JSC] has progressively developed and reconfigured the GeoLab hardware and software interfaces and developed test objectives, which were to 1) determine requirements and strategies for sample handling and prioritization for geological operations on other planetary surfaces, 2) assess the scientific contribution of selective in-situ sample characterization for mission planning, operations, and sample prioritization, 3) evaluate analytical instruments and tools for providing efficient and meaningful data in advance of sample return and 4) identify science operations that leverage human presence with robotic tools. In the first year of tests (2010), GeoLab examined basic glovebox operations performed by one and two crewmembers and science operations performed by a remote science team. The 2010 tests also examined the efficacy of basic sample characterization [descriptions, microscopic imagery, X-ray fluorescence (XRF) analyses] and feedback to the science team. In year 2 (2011), the GeoLab team tested enhanced software and interfaces for the crew and science team (including Web-based and mobile device displays) and demonstrated laboratory configurability with a new diagnostic instrument (the Multispectral Microscopic Imager from the JPL and Arizona State University). In year 3 (2012), the GeoLab team installed and tested a robotic sample manipulator and evaluated robotic-human interfaces for science operations.

Evans, Cynthia↗
DOE OSTI2026

lanl/bacterial-classification

bacterial-classification is a sub repository of the Intelligent Immunity project specific to training and testing machine learning models for bacterial classification (Gram-positive, Gram-negative, and non-bacterial samples). Specifically, this repository aims to compare ML classification performance across different dataset curation strategies.

Mancuso, Marina [Los Alamos National Laboratory]↗
DOE OSTI2014

Metazen – metadata capture for metagenomes

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Using X-Ray Computed Tomography to Catalog Rock Fragments in Apollo Drive Tube 73002

Overview: The Apollo missions collected 382 kg of rock, regolith, and core samples from six locations on the nearside of the Moon. Approximately 84% by mass of the Apollo collection remains in pristine condition within the curation facility at Johnson Space Center (i.e., never allocated, continuously stored in dry-N2 purged cabinets, exposure history restricted to Teflon, stainless steel, and Al-metal). Although most Apollo samples have been well characterized, there are several types of samples that have remained wholly or largely unstudied since their return, and/or that have been cu-rated under special conditions, e.g., frozen samples, samples stored in He-purged environment, and previously unopened drive tubes. NASA solicited proposals for the Apollo Next Generation Sample Analysis Pro-gram (ANGSA), and 9 teams were selected to study a subset of the unopened and frozen samples [1]. The first sample opened as part of the ANGSA pro-gram was drive tube 73002. This was originally a ~30 cm long, 4 cm diameter drive tube collected on a land-slide deposit near Lara Crater at the Apollo 17 landing site. It was part of a ~60 cm long double drive tube collected, and the bottom half of the tube (73001) was sealed under vacuum on the Moon [2]. Prior to opening sample 73002, the sample was imaged with a high resolution X-ray Computed Tomography (XCT) scan of the entire tube [3], which provided invaluable information during the dissection process [4]. In addition to the pre-dissection XCT scans, individual >4 mm particles were separated from the 73002 regolith during processing and scanned at high resolution by XCT. Here we pre-sent the initial lithologic classification of 134 individual >4 mm rock fragments separated from the 73002 core during the dissection process. Methodology: Drive tube 73002 was manually dissected in 0.5 cm depth intervals in three passes (Fig. 1) [4,5]. Each interval from pass 1 and 2 was sieved to <1 mm and >1 mm size fractions, and >1 mm particles were further manually subdivided into 1-2, 2-4, 4-10, and >10 mm size fractions. Pass 3 was not sieved, but >10 mm clasts were separated manually. Each 4-10 mm and >10 mm fragment was individually weighed, triply bagged in Teflon, and scanned by XCT. There are 60 rock fragments in Pass 1, 64 rock fragments in Pass 2 (from the 4-10 mm and >10 mm size fractions), and 8 rock fragments from Pass 3 (>10 mm size fraction). Each individually bagged rock fragment was scanned using the 180 kV nano-focus transmission source on the Nikon XTH 320 XCT system at NASA Johnson Space Center [6]. Scanning conditions varied considerably for individual particles, in large part be-cause of the large variation in size (0.008-19.623 g). All scans fell within the following range of scan conditions: 2.8-20.6 um voxel size; 90-155 kV voltage; 18-39 uA current; 1891-3141 projections; and 902-2000 slices. Results and Discussion: The 132 rock fragments from sample 73002 fall into the following general cat-gories: agglutinates (n = 6); basalts (13); impact melts (5); impact melt breccias (IMB; 42); regolith breccias (62); and soil breccias (4); see Figure 2 for representative examples of each lithology. Within most of these broad lithologic groups are recognizable subgroups. For example, a significant portion of regolith breccia fragments contain some agglutinate-like glass (n = 9) or are dilithologic (7) because they contain a single large clast (~50% or more by volume). Subgroups can be based on similarities to previously identified lunar lithologies, such as high-Ti basalts (9) and VLT basalts (4; Fig. 3), or based on commonly seen features within the fragments, such as poikilitic ilmenite IMB (10), ilmenite-lath IMB (12), or vesicular IMB (11) “groups”. Particles in the same “group” are not necessarily intended to be genetically related, but rather identify particles that are similar and that follow-up studies can classify in more detail [7]. Conclusion: Identification of lithologies based on XCT is a powerful tool, but a more absolute classification will sometimes require additional textural information from thin sections (e.g., glassy-matrix regolith vs. impact-melt vs. granulitic breccia) or quantitative mineral compositions (e.g., basalt vs. monomict breccia).

R A Zeigler↗
DOE OSTI2026

Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction

Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

Kok, C [Lawrence Livermore National Laboratory (LL↗
DOE OSTI2015

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13 21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.

60 APPLIED LIFE SCIENCES↗