Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence contamination”

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 127 records · Page 7

Materials and manufacturing processes for increased life/reliability

Improvements in both quality and durability of disk raw material for both military and commercial engines necessitated an entirely new concept in raw material process control which imposes careful selection, screening and sampling of the basic alloy ingredients, followed by careful monitoring of the melting parameters in all phases of the vacuum melting sequence. Special care is taken to preclude solidification conditions that produce adverse levels of segregation. Melt furnaces are routinely cleaned and inspected for contamination. Ingots are also cleaned and inspected before entering the final melt step.

Duttweiler, R. E.↗

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

59 BASIC BIOLOGICAL SCIENCES↗

The surroundings of the Milky Way globular cluster NGC 6809

ABSTRACT We study the outer regions of the Milky Way globular cluster NGC 6809 based on Dark Energy Camera observations, which reach nearly 6 mag below the cluster main-sequence (MS) turn-off. In order to unveil its fainter outermost structure, we built stellar density maps using cluster MS stars, once the contamination of field stars was removed from the cluster colour–magnitude diagram. We found that only the resulting stellar density map for the lightest stars exhibits some excesses of stars at opposite sides from the cluster centre that diminish soon thereafter at ∼ 0.32°.Studied globular clusters with apogalactic distances smaller than that of NGC 6809 (5.5 kpc) do not have observed tidal tails. The lack of detection of tidal tails in the studied inner globular cluster sample could be due to the reduced diffusion time of tidal tails by the kinematically chaotic nature of the orbits of these globular clusters, thus shortening the time interval during which the tidal tails can be detected. Further investigations with an enlarged cluster sample are needed to confirm whether chaotic and non-chaotic orbits are responsible for the existence of globular clusters with tidal tails and those with extra-tidal features that are different from tidal tails or without any signatures of extended stellar density profiles.

Piatti, Andrés E.↗

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Genomes_SET2_178 - Shared

The dataset consists of 178 bacterial genomes in total. Of these, 145 genomes were drawn from published literature linked to Biolog Gen III growth data, while 33 genomes came from soil isolates collected at the Cedar Creek Ecosystem Science Research Reserve (CCESR) in Minnesota. The isolates were sequenced on an Illumina HiSeq platform (~50× coverage), assembled with Megahit, and annotated using RAST at PATRIC, with strict quality filtering (<90% completeness or >5% contamination).

59 BASIC BIOLOGICAL SCIENCES↗

Insights From Routine Microbiological Monitoring of Air in Astromaterials Curation Cleanrooms

NASA maintains nine separate cleanrooms at the Johnson Space Center to curate and preserve astromaterials samples. Routine microbial monitoring of the surfaces in these cleanrooms began in 20181. Until recently, materials compatibility requirements prevented monitoring airborne biological particles in all but one of these cleanrooms. New astromaterials collections from carbon rich asteroids are more susceptible to biological degradation than previous collections. Therefore, it is important to monitor the bioburden in the air and on surfaces in these labs. Establishing a comprehensive microbial monitoring program will help inform the monitoring and curation plans for Mars sample return which will include samples that are extremely biologically sensitive. In April of 2022 we began routinely collecting air samples in seven of the nine curation cleanrooms (Meteorite ISO 7 equivalent, Lunar ISO 6 equivalent, Stardust, Hayabusa2, OSIRIS-REx ISO 5 equivalent, and Genesis ISO 4 equivalent) using a sampling device that collects airborne biological particles on an electret filter instead conventional sampler that collect cells in a liquid media or onto organic rich Petri dishes. Electret is a generic term for electrostatically charged media. The charge on these materials increases particle trapping when compared to non-charged filters of similar thickness. N95 respirators also use electret filters. This dry sample collection method allows us to meet materials requirements for all the curation labs and reduces the risk of inadvertently introducing contamination as part of our monitoring effort. This method also allows us to preserve a portion of each sample for DNA extraction and next generation sequencing. DNA sequencing helps us to characterize the portion of the cleanroom microbiome that we cannot culture. We will present the results of our first 8 months of monitoring, compare these results to particle counts in the labs and to measurements made directly onto Petri dishes when possible. We will also make recommendations for modifications to the sampling method to improve sampling efficiency and preserve diversity.

A. B. Regberg↗

Planetary Protection at Marshall Space Flight Center

Introduction: NASA Marshall Space Flight Center (MSFC) is historically known for its role in propulsion. While this is still the mainstay of MSFC’s expertise, many unique capabilities exist at MSFC which pertain to Planetary Protection (PP), including 1) identifying PP threats, and 2) developing novel methods to neutralize those threats. Furthermore, because these capabilities exist among diverse groups at MSFC, this work promotes collaboration both within and outside MSFC to expand and develop PP studies related to a full spectrum of NASA research, design, manufacture, and test interests. This abstract describes the PP research ongoing at MSFC and describes how it contributes to NASA’s overall PP objectives. Microbial Identification in Cleanrooms: One of the greatest threats to successful implementation of PP requirements is recontamination post bioburden reduction. One method to prevent recontamination is to keep the spacecraft in clean environments (i.e. cleanrooms) as much as possible during assembly and integration. However, cleanrooms are not without their own sources of contamination, which is why NASA is interested in monitoring the cleanliness of cleanrooms and characterizing the microbial species present. Such information allows a greater understanding of the resistance of these microbes to cleaning methods, as well as the risk of their contaminating the targeted planetary body of a given mission. MSFC has multiple cleanrooms of various ISO cleanliness levels onsite. We sampled the air and surfaces of three of these rooms, isolated microbes, and then sequenced the 16S rRNA gene or ITS region of the 18S rRNA gene for bacterial and fungal isolates, respectively. This has resulted in a microbial library which currently includes nearly 100 isolates. Microbial Enumeration of Spacecraft Materials: Currently, there are only a couple bioburden reduction methods approved by NASA, and often the harshness of these methods presents additional concerns or risks related to material properties. The goal of this research is to assess the microbial content of solid rocket motor (SRM) materials potentially used for lander missions. This work aims to more accurately define the risk of planetary contamination by providing empirical data associated with commonly used SRM raw materials. In this study, we pulverized nonmetallic SRM materials using a cryogenic grinder, then analyzed the resulting substrate for microbial colony forming units (CFU). We found that many SRM nonmetallic materials do not harbor detectable bioburden, though a range existed depending on the material. The results from this work provide quantitative data to potentially reduce concerns of contamination, while also providing a foundation for follow up studies into additional sterilization methods and molecular identification of contaminating microbes. Space Environmental Effects on Microbial Survival: One potential area of microbial reduction is the space environment. Understanding the survivability of hardy microbes in space-like conditions is a crucial first step in answering how space may reduce bioburden and if it can be relied upon for adherence to PP requirements. This work studied the effects of ultraviolet (UV) and ionizing radiation on survival of Bacillus atrophaeus spores. Microbes were dried on relevant polymeric materials then exposed to space environmental stressors. Coupons were submerged in water, diluted, and plated to determine survival compared with controls. We found that both UV and ionizing radiation were capable of reducing viability by nearly 99%, but there were still survivors, some with changed morphology indicating resistance mechanisms within certain cells. Manufacturing credit: Finally, given the above-mentioned limitations of the NASA-approved bioburden reduction methods, there is interest in understanding if manufacturing processes may provide enough bioburden reduction without additional PP-specific bakeouts. For instance, some material additives may be antimicrobial. Given this, we investigated the effects of several commonly used rubber additives on the growth of B. atrophaeus spores. We found that some of the materials inhibited growth of the spores, possibly supporting the use of these additives on missions with PP constraints. Future work into manufacturing credit for bioburden reduction includes inoculation of green insulation with B. atrophaeus spores, followed by a typical cure. Thermal profiles will be verified for appropriate temperature and durations to meet PP requirements, and cured samples will be analyzed using a cryogenic grinder to determine survivability of spores.

Chelsi D. Cassilly↗

A global perspective on bacterial diversity in the terrestrial deep subsurface

While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20% of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8% in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗

Microbiomes of commercially-available pine nuts and sesame seeds

Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

The eROSITA Final Equatorial-Depth Survey (eFEDS)

In 2019, the eROSITA telescope on board the Russian-German satellite Spectrum-Roentgen-Gamma (SRG) began to perform a deep all-sky X-ray survey with the aim of identifying ~100 000 clusters and groups over the course of four years. As part of its performance verification phase, a ~140 deg 2 survey, called eROSITA Final Equatorial-Depth Survey (eFEDS), was performed. With a depth typical of the all-sky survey after four years, it allows tests of tools and methods as well as improved predictions for the all-sky survey. As part of this effort, a catalog of 542 X-ray selected galaxy group and cluster candidates was compiled. Here, in this paper, we present the optical follow-up, with the aim of providing redshifts and cluster confirmation for the full sample. Furthermore, we aim to provide additional information on the dynamical state, richness, and optical center of the clusters. Finally, we aim to evaluate the impact of optical cluster confirmation on the purity and completeness of the X-ray selected sample. We used optical imaging data from the Hyper Suprime-Cam Subaru Strategic Program and from the Legacy Survey to identify optical counterparts to the X-ray detected cluster candidates. We make use of the multi-component matched filter cluster confirmation tool (MCMF), as well as of the optical cluster finder CAMIRA to derive cluster redshifts and richnesses. MCMF provided the probabilities with which an optical structure would be a chance superposition with the X-ray candidate. These probabilities were used to identify the best optical counterpart as well as to confirm an X-ray candidate as a cluster. The impact of this confirmation process on catalog purity and completeness was estimated using optical to X-ray scaling relations as well as simulations. The resulting catalog was furthermore matched with public group and cluster catalogs. Optical estimators of the cluster dynamical state were constructed based on density maps of the red-sequence galaxies at the cluster redshift. By providing redshift estimates for all 542 candidates, we construct an optically confirmed sample of 477 clusters and groups with a residual contamination of 6%. Of these, 470 (98.5%) are confirmed using MCMF, and 7 systems are added through cross-matching with spectroscopic group catalogs. Using observable-to-observable scaling and the applied confirmation threshold, we predict that 8 ± 2 real systems have been excluded with the MCMF cut required to build this low-contamination sample. This number agrees well with the 7 systems found through cross-matching that were not confirmed with MCMF. The predicted redshift and mass distribution of this catalog agree well with simulations. Thus, we expect that these 477 systems include >99% of all true clusters in the candidate list. Using an MCMF-independent method, we confirm that the catalog contamination of the confirmed subsample is 6 ± 3%. Application of the same method to the full candidate list yields 17 ± 3%, consistent with estimates coming from the fraction of confirmed systems of ~17% and with expectations from simulations of ~20%. We also present a sample of merging cluster candidates based on the derived estimators of the cluster dynamical state.

79 ASTRONOMY AND ASTROPHYSICS↗

Atacama Rover Astrobiology Drilling Studies Project: Final Year

The Atacama Rover Astrobiology Drilling Studies (ARADS) project, a simulated Mars rover biomarker detection mission, was iteratively developed over four years from 2015 -2019, including three NASA centers, the Centro de Astrobiologia, Johns Hopkins University, Honeybee Robotics, Maxar and the University of Antofagasta. The final (4th) ARADS field season, in 2019, tested an integrated mobile life-prospecting platform loosely inspired by the 2000’s Astrobiology Field Laboratory concept, with a 1m rotary-percussive drill and sample transfer robot arm that fed three astrobiology instruments operating in-situ on the KREX2 medium rover prototype. A fourth instrument was field tested earlier in 2019 due to flight mission requirements. In the final ARADS field deployment in September 2019, the project conducted a remote mission operation simulation (Stoker 2022)demonstrating sample drilling, acquisition and transfer into the rover instruments (while minimizing cross-contamination), performing in-situ analysis of the samples, and returning the results to a remote science operations team(which commanded the daily science goals and uploaded operations sequences).

astrobiology↗

KBase Narrative - Supplemental Data for "Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes"

Here we provide the complete set of circular elements produced by SCAPP from metagenomic data that may represent mobile genetic elements (MGEs). For the publication, these sequences were de-replicated within the high [U] and low [U] sample sets. Additionally, 98 of the circular elements were removed for downstream analysis due to high suspicion of being (1) chloroplast or mitochondrial sequences or (2) erroneously circularized long repeat regions. The complete list of circular elements used for the analysis along with metadata can be found in Tables S5 and S6.

Goff, Jennifer↗

Hollow-Sphere Production Line

After initial formation, spheroids processed without contaminating touch of solid objects. Spheroid in process supported by acoustic levitation at each work station and transported between stations by combination of acoustic levritation and acoustic propulsion. Automatic sequence of target-pellet fabication allows no contact of solid ojbect with spheroids in process. Potential for manufacture of precise microcapsules for catalysts and medications.

Lee, M. C.↗

The International Space Station Urine Monitoring System (UMS)

A device capable of making in-flight volume measurements of single void urine samples, the Urine Monitoring System (UMS), was developed and flown on seven U.S. Space Shuttle missions. This device provided volume data for each urine void from multiple crewmembers and allowed samples of each to be taken and returned to Earth for post-flight analysis. There were a number of design flaws in the original instrument including the presence of liquid carry-over producing invalid "actual" micturition volumes and cross-contamination between successive users from residual urine in "dead" spots". Additionally, high or low volume voids could not be accurately measured, the on-orbit calibration and nominal use sequence was time intensive, and the unit had to be returned and disassembled to retrieve the volume data. These problems have been resolved in a new version, the International Space Station (ISS) UMS, that has been designed to provide real-time in-flight volume data with accuracy and precision equivalent to measurements made on Earth and the ability to provide urine samples that are unadulterated by the device. Originally conceived to be interfaced with a U.S.-built Waste Collection System (WCS), the unit now has been modified to interface with the Russian-supplied Sanitary Hygiene Device (ASY). The ISS UMS provides significant advantages over the current method of collecting urine samples into Urine Collection Devices (UCDs), from which samples are removed and returned to Earth for analyses. A significant future advantage of the UMS is that it can provide an interface to analytical instrumentation that will allow real-time measurement of urine bioanalytes allowing monitoring of crewmember health status during flight and the ability to provide medical interventions based on the results of these measurements. Currently, the ISS UMS is scheduled to launch along with Node-3 on STS-130 (20A) in December 2009. UMS will be installed and scientific/functional verification completed prior to placing the instrument into operation. Samples collected during the verification sequence will be returned for analyses on STS-131 (19A) currently scheduled for launch in March 2010. The presence of a UMS on ISS will provide the capability to conduct additional collaborative human life science investigations among the ISS International Partners.

Feeback, Daniel L.↗

Resolving the xi Boo Binary with Chandra, and Revealing the Spectral Type Dependence of the Coronal "Fip Effect"

On 2008 May 2, Chandra observed the X-ray spectrum of xi Boo (G8 V+K4 V), resolving the binary for the first time in X-rays and allowing the coronae of the two stars to be studied separately. With the contributions of ξ Boo A and B to the system's total X-ray emission now observationally established (88.5% and 11.5% respectively), consideration of mass loss measurements for GK dwarfs of various activity levels (including one for xi Boo) leads to the surprising conclusion that xi Boo B may dominate the wind from the binary, with xi Boo A's wind being very weak despite its active corona. Emission measure (EM) distributions and coronal abundances are computed for both stars and compared with Chandra measurements of other moderately active stars with G8-K5 spectral types, all of which exhibit a narrow peak in EM near log T = 6.6, indicating that the coronal heating process in these stars has a strong preference for this temperature. As is the case for the Sun and many other stars, our sample of stars shows coronal abundance anomalies dependent on the first ionization potential (FIP) of the element. We see no dependence of the degree of FIP effect on activity, but there is a dependence on spectral type, a correlation that becomes more convincing when moderately active main-sequence stars with a broader range of spectral types are considered. This clear dependence of coronal abundances on spectral type weakens if the stellar sample is allowed to be contaminated by evolved stars, interacting binaries or extremely active stars with logLX 29, explaining why this correlation has not been recognized in the past.

CHANDRA↗

The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.

59 BASIC BIOLOGICAL SCIENCES↗

Equations of motion of a constrained split fairing system during opening.

Description of a constrained split fairing technique for avoiding contamination of a sounding rocket's payload environment by an uncontained explosive actuation device. The development is presented of the equations of motion of the fairing halves during the opening sequence assumed to occur above the sensible atmosphere. It is believed that a significant insight into the general motion results from the solution obtained.

Saunders, R. C., Jr.↗