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NASA NTRS2009

Discrimination of Spore-Forming Bacilli Using spoIVA

A method of discriminating between spore-forming and non-spore-forming bacteria is based on a combination of simultaneous sporulation-specific and non-sporulation-specific quantitative polymerase chain reactions (Q-PCRs). The method was invented partly in response to the observation that for the purposes of preventing or reducing biological contamination affecting many human endeavors, ultimately, only the spore-forming portions of bacterial populations are the ones that are problematic (or, at least, more problematic than are the non-spore-forming portions). In some environments, spore-forming bacteria constitute small fractions of the total bacterial populations. The use of sporulation-specific primers in Q-PCR affords the ability to assess the spore-forming fraction of a bacterial population present in an environment of interest. This assessment can provide a more thorough and accurate understanding of the bacterial contamination in the environment, thereby making it possible to focus contamination- testing, contamination-prevention, sterilization, and decontamination resources more economically and efficiently. The method includes the use of sporulation-specific primers in the form of designed, optimized deoxyribonucleic acid (DNA) oligonucleotides specific for the bacterial spoIVA gene (see table). [In "spoIVA," "IV" signifies Roman numeral four and the entire quoted name refers to gene A for the fourth stage of sporulation.] These primers are mixed into a PCR cocktail with a given sample of bacterial cells. A control PCR cocktail into which are mixed universal 16S rRNA primers is also prepared. ["16S rRNA" denotes a ribosomal ribonucleic acid (rRNA) sequence that is common to all organisms.] Following several cycles of heating and cooling according to the PCR protocol to amplify amounts of DNA molecules, the amplification products can be analyzed to determine the types of bacterial cells present within the samples. If the amplification product is strong, relative to the product of a control PCR sequence, then it is concluded that the bacterial population in the sample consists predominantly of spore-forming cells. If the amplification product is weak or nonexistent, then it is concluded that the bacterial population in the sample consists predominantly or entirely of non-spore-forming cells.

Venkateswaran, Kasthuri↗

NASA NTRS1997

Mir Cooperative Solar Array Flight Performance Data and Computational Analysis

The Mir Cooperative Solar Array (MCSA) was developed jointly by the United States (US) and Russia to provide approximately 6 kW of photovoltaic power to the Russian space station Mir. The MCSA was launched to Mir in November 1995 and installed on the Kvant-1 module in May 1996. Since the MCSA photovoltaic panel modules (PPMs) are nearly identical to those of the International Space Station (ISS) photovoltaic arrays, MCSA operation offered an opportunity to gather multi-year performance data on this technology prior to its implementation on ISS. Two specially designed test sequences were executed in June and December 1996 to measure MCSA performance. Each test period encompassed 3 orbital revolutions whereby the current produced by the MCSA channels was measured. The temperature of MCSA PPMs was also measured. To better interpret the MCSA flight data, a dedicated FORTRAN computer code was developed to predict the detailed thermal-electrical performance of the MCSA. Flight data compared very favorably with computational performance predictions. This indicated that the MCSA electrical performance was fully meeting pre-flight expectations. There were no measurable indications of unexpected or precipitous MCSA performance degradation due to contamination or other causes after 7 months of operation on orbit. Power delivered to the Mir bus was lower than desired as a consequence of the retrofitted power distribution cabling. The strong correlation of experimental and computational results further bolsters the confidence level of performance codes used in critical ISS electric power forecasting. In this paper, MCSA flight performance tests are described as well as the computational modeling behind the performance predictions.

Kerslake, Thomas W.↗

NASA NTRS2012

Calibration and Sequence Development Status for the Sample Analysis at Mars Investigation on the Mars Science Laboratory

The measurement goals of the Sample Analysis at Mars (SAM) instrument suite on the "Curiosity" Rover of the Mars Science Laboratory (MSL) include chemical and isotopic analysis of organic and inorganic volatiles for both atmospheric and solid samples [1,2]. SAM directly supports the ambitious goals of the MSL mission to provide a quantitative assessment of habitability and preservation in Gale crater by means of a range of chemical and geological measurements [3]. The SAM FM combined calibration and environmental testing took place primarily in 2010 with a limited set of tests implemented after integration into the rover in January 2011. The scope of SAM FM testing was limited both to preserve SAM consumables such as life time of its electromechanical elements and to minimize the level of terrestrial contamination in the SAM instrument. A more comprehensive calibration of a SAM-like suite of instruments will be implemented in 2012 with calibration runs planned for the SAM testbed. The SAM Testbed is nearly identical to the SAM FM and operates in a ambient pressure chamber. The SAM Instrument Suite: SAM's instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). Gas Chromatography Mass Spectrometry is designed for identification of even trace organic compounds. The TLS [5] secures the C, H, and O isotopic composition in carbon dioxide, water, and methane. Sieved materials are delivered from the MSL sample acquisition and processing system to one of68 cups of the Sample Manipulation System (SMS). 59 of these cups are fabricated from inert quartz. After sample delivery, a cup is inserted into one of 2 ovens for evolved gas analysis (EGA ambient to >9500C) by the QMS and TLS. A portion of the gas released can be trapped and subsequently analyzed by GCMS. Nine sealed cups contain liquid solvents and chemical derivatization or thermochemolysis agents to extract and transform polar molecules such as amino acids, nucleobases, and carboxylic acids into compounds that are sufficiently volatile to transmit through the GC columns. The remaining 6 cups contain calibrants. SAM FM Calibration Overview: The SAM FM calibration in the Mars chamber employed a variety of pure gases, gas mixtures, and solid materials. Isotope calibration runs for the TLS utilized 13C enriched C02 standards and 0 enriched CH4. A variety of fluorocarbon compounds that spanned the entire mass range of the QMS as well as C3-C6 hydrocarbons were utilized for calibration of the GCMS. Solid samples consisting of a mixture of calcite, melanterite, and inert silica glass either doped or not with fluorocarbons were introduced into the SAM FM cups through the SAM inlet funnel/tube system.

Mahaffy, Paul R.↗

DOE OSTI2026

Plasma-assisted atomic layer etching of single-crystal diamond

Applications of near-surface nitrogen-vacancy (NV) centers in diamond are often limited by surface defects created during processing. Understanding and controlling plasma-induced surface damage is important for preserving the optical and spin properties of diamond NV centers. We report molecular dynamics simulations of a novel form of plasma-aided atomic layer etching of diamond. In this proposed scheme, the initial surface modification step consists of Ar + ion bombardment. This creates an amorphous layer at the surface, the thickness of which is controlled by the ion energy. Amorphization is known to help smooth the surface, at least locally, and would also serve to sputter clean an initially contaminated surface. A second step impacts the amorphous carbon layer with O + between about 1 and 5 eV. Simulations show that this energy range will remove the amorphous carbon but will not etch the underlying diamond. Though this energy range is not trivial to achieve in a conventional low-temperature plasma, potential methods for creating these low-energy O + ions are discussed. In addition to a-C etching, the O + impacts are predicted to remove any isolated (100) diamond terraces by selectively attacking the edges of the terraces. The proposed atomic layer etching (ALE) approach reverses the conventional ALE sequence in which the surface modification step is usually chemical modification (oxidation in this case), followed by a removal step using Ar + impacts. This plasma ALE procedure is predicted to create a diamond surface that is atomically flat and defect free.

Draney, J. S. [Princeton University, NJ (United St↗

NASA NTRS2011

Low-Outgassing Photogrammetry Targets for Use in Outer Space

A short document discusses an investigation of materials for photogrammetry targets for highly sensitive optical scientific instruments to be operated in outer space and in an outer-space-environment- simulating thermal vacuum chamber on Earth. A key consideration in the selection of photogrammetry-target materials for vacuum environments is the need to prevent contamination that could degrade the optical responses of the instruments. Therefore, in addition to the high levels and uniformity of reflectivity required of photogrammetry-target materials suitable for use in air, the materials sought must exhibit minimal outgassing. Commercially available photogrammetry targets were found to outgas excessively under the thermal and vacuum conditions of interest; this finding prompted the investigators to consider optically equivalent or superior, lower-outgassing alternative target materials. The document lists several materials found to satisfy the requirements, but does not state explicitly whether the materials can be used individually or must be combined in the proper sequence into layered target structures. The materials in question are an aluminized polyimide tape, an acrylic pressure- sensitive adhesive, a 500-A-thick layer of vapor-deposited aluminum, and spherical barium titanate glass beads having various diameters from 20 to 63 microns..

Gross, Jason N.↗

DOE OSTI2024

Transfer of beef bacterial communities onto food-contact surfaces

Introduction Food spoilage and pathogenic bacteria on food-contact surfaces, especially biofilm-forming strains, can transfer to meats during processing. The objectives of this study were to survey the bacterial communities of beef cuts that transfer onto two commonly used food-contact surfaces, stainless steel (SS) and high-density polyethylene (HDPE) and identify potentially biofilm-forming strains. Methods Top round, flank, chuck, and ground beef were purchased from 3 retail stores. SS and HDPE coupons (approximately 2cm × 5cm) were placed on beef portions (3h, 10°C), after which, the coupons were submerged halfway in PBS (24h, 10°C). Bacteria from the beef cuts and coupon surfaces ( n = 3) were collected, plated on tryptic soy agar plates and incubated (5 days, 25°C). Bacterial isolates were identified by 16S rRNA gene amplicon sequencing and assayed for biofilm formation using a crystal violet binding (CV) assay (72h, 10°C). Additionally, beef and coupon samples were collected for bacterial community analysis by 16S rRNA gene amplicon sequencing. Results and discussion Sixty-one of 972 beef isolates, 29 of 204 HDPE isolates, and 30 of 211 SS isolates were strong biofilm-formers (Absorbance>1.000 at 590 nm in the CV assay). Strong-binding isolates identified were of the genera Pseudomonas , Acinetobacter , Psychrobacter , Carnobacterium , and Brochothrix . Coupon bacterial communities among stores and cuts were distinct ( p < 0.001, PERMANOVA), but there was no distinction between the communities found on HDPE or SS coupons ( p > 0.050, PERMANOVA). The bacterial communities identified on the coupons may help determine the communities capable of transferring and colonizing onto surfaces, which can subsequently cross-contaminate foods.

Guron, Giselle K. P.↗

NASA NTRS2006

Boom Rendezvous Alternative Docking Approach

Space rendezvous and docking has always been attempted with primarily one philosophic methodology. The slow matching of one vehicle's orbit by a second vehicle and then a final closing sequence that ends in matching the orbits with perfect precision and with near zero relative velocities. The task is time consuming, propellant intensive, risk inherent (plume impingement, collisions, fuel depletion, etc.) and requires substantial hardware mass. The historical background and rationale as to why this approach is used is discussed in terms of the path-not-taken and in light of an alternate methodology. Rendezvous and docking by boom extension is suggested to have inherent advantages that today s technology can readily exploit. Extension from the primary spacecraft, beyond its inherent large inertia, allows low inertia connections to be made rapidly and safely. Plume contamination issues are eliminated as well as the extra propellant mass and risk required for the final thruster (docking) operations. Space vehicle connection hardware can be significantly lightened. Also, docking sensors and controls require less fidelity; allowing them to be more robust and less sensitive. It is the potential safety advantage and mission risk reduction that makes this approach attractive, besides the prospect of nominal time and mass savings.

Bonometti, Joseph A.↗

DOE OSTI2020

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7±19.1 and 36.5±10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2023

Using Mylar-Insulated Cryopumping Panels to Improve Vacuum Level During Warm Temperature Testing at JSCs Large Thermal Vacuum Facilities

The Johnson Space Center’s Space Environment Simulation Lab (SESL) has both Chamber A, the world’s largest purpose-built thermal vacuum chamber capable of creating deep space conditions, and Chamber B, the largest human rated thermal vacuum chamber. A unique design feature of these chambers is the gaseous helium cryopumping panels within the liquid nitrogen shroud. This shroud is used to bring the chamber to cryogenic temperatures while the cryopumping panels trap gasses using their large surface area in order to create a high vacuum environment of 5*10^-6 Torr. In preparation for the James Webb Space Telescope (JWST) flight test, a series of functionals required the chamber to run at higher temperatures, and therefore did not need active cooling from the liquid nitrogen shroud. During testing, cryopumping panels were used to mitigate contamination during this main shroud warm-up. One of the cryopumping panels in Chamber A was covered with several layers of aluminized mylar in order to thermally protect the zone from the warmed shroud. This strategy was effective and became part of operations during JWST testing. Currently, Chamber B has requests for both commercial and NASA space suit tests at both high and low temperatures to accurately generate thermal models. High temperature tests would greatly benefit from simultaneous shroud warming and the high vacuum environment provided by the cryopumping panels. This paper will quantitatively define the thermal loads on the panels used in previous Chamber A warm up sequences. Additionally, this report will perform a thermal analysis to judge the feasibility of adding layers of aluminized mylar to the cryopumping panels of Chamber B.

Cryogenics↗

NASA NTRS2023

Using Mylar-Insulated Cryopumping Panels to Improve Vacuum Level During Warm Temperature Testing at JSC's Large Thermal Vacuum Facilities

Cryogenics↗

NASA NTRS1999

Evidence of SV40 infections in hospitalized children

Simian virus 40 (SV40) is known to have contaminated poliovirus vaccines used between 1955 and 1963. Accumulating reports have described the presence of SV40 DNA in human tumors and normal tissues, although the significance of human infections by SV40 is unknown. We investigated whether unselected hospitalized children had evidence of SV40 infections and whether any clinical correlations were apparent. Serum samples were examined for SV40 neutralizing antibody using a specific plaque reduction test; of 337 samples tested, 20 (5.9%) had antibody to SV40. Seropositivity increased with age and was significantly associated with kidney transplants (6 of 15 [40%] positive, P < .001). Many of the antibody-positive patients had impaired immune systems. Molecular assays (polymerase chain reaction and DNA sequence analysis) on archival tissue specimens confirmed the presence of SV40 DNA in 4 of the antibody-positive patients. This study, using 2 independent assays, shows the presence of SV40 infections in children born after 1980. We conclude that SV40 causes natural infections in humans.

NASA Discipline Regulatory Physiology↗

NASA NTRS2023

Using Mylar-Insulated Cryopumping Panels to Improve Vacuum Level During Warm Temperature Testing at JSC's Large Thermal Vacuum Facilities

Johnson Space Center’s Space Environment Simulation Lab (SESL) has both Chamber A, the world’s largest purpose-built thermal vacuum chamber capable of creating deep space conditions, and Chamber B, the largest human rated thermal vacuum chamber. A unique design feature of these chambers is the gaseous helium cryopumping panels within the liquid nitrogen shroud. This shroud is used to bring the chamber to cryogenic temperatures while the cryopumping panels trap gasses on its surface area to create a high vacuum environment of 5*10-6 Torr. In preparation for the James Webb Space Telescope (JWST) flight test, a series of functionals required the chamber to run at higher temperatures, and therefore did not need active cooling from the liquid nitrogen shroud. During testing, cryopumping panels were used to mitigate contamination during this main shroud warm-up. One of the cryopumping panels in Chamber A was covered with several layers of aluminized mylar to thermally protect the zone from the warmed shroud. This strategy was effective and became part of operations during JWST testing. Currently, Chamber B has requests for both commercial and NASA space suit tests at both high and low temperatures to validate thermal models. High temperature tests could benefit from reduced heater demand with an insulated shroud while still sustaining the high vacuum environment provided by the cryopumping panels. This paper will quantitatively define the thermal loads on the panels used in previous Chamber A warm up sequences. Additionally, this report will perform thermal analyses to assess the feasibility of adding layers of aluminized mylar to the cryopumping panels of Chamber B.

Cryogenics↗

NASA NTRS1993

STS-55 pad abort: Engine 2011 oxidizer preburner augmented spark igniter check valve leak

The STS-55 initial launch attempt of Columbia (OV102) was terminated on KSC launch pad A March 22, 1993 at 9:51 AM E.S.T. due to violation of an ME-3 (Engine 2011) Launch Commit Criteria (LCC) limit exceedance. The event description and timeline are summarized. Propellant loading was initiated on 22 March, 1993 at 1:15 AM EST. All SSME chill parameters and launch commit criteria (LCC) were nominal. At engine start plus 1.44 seconds, a Failure Identification (FID) was posted against Engine 2011 for exceeding the 50 psia Oxidizer Preburner (OPB) purge pressure redline. The engine was shut down at 1.50 seconds followed by Engines 2034 and 2030. All shut down sequences were nominal and the mission was safely aborted. The OPB purge pressure redline violation and the abort profile/overlay for all three engines are depicted. SSME Avionics hardware and software performed nominally during the incident. A review of vehicle data table (VDT) data and controller software logic revealed no failure indications other than the single FID 013-414, OPB purge pressure redline exceeded. Software logic was executed according to requirements and there was no anomalous controller software operation. Immediately following the abort, a Rocketdyne/NASA failure investigation team was assembled. The team successfully isolated the failure cause to the oxidizer preburner augmented spark igniter purge check valve not being fully closed due to contamination. The source of the contaminant was traced to a cut segment from a rubber O-ring which was used in a fine clean tool during valve production prior to 1992. The valve was apparently contaminated during its fabrication in 1985. The valve had performed acceptably on four previous flights of the engine, and SSME flight history shows 780 combined check valve flights without failure. The failure of an Engine 3 (SSME No. 2011) check valve to close was sensed by onboard engine instruments even though all other engine operations were normal. This resulted in an engine shutdown and safe sequential shutdown of all three engines prior to ignition of the solid boosters.

Source record↗

DOE OSTI2020

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

Riparian floodplains represent an interaction zone between the terrestrial subsurface and rivers, where regional groundwater flows, infiltration, and evapotranspiration drive mixing of water and import/export of nutrients and contaminants. These dynamics create seasonally transient redox conditions that drive biogeochemical transformations, which strongly modify groundwater quality. Microbial responses to changing hydrological conditions are perhaps the critical step connecting hydrology to geochemical transformations and groundwater quality, yet are not well understood. We aimed to address this knowledge gap by monitoring seasonal transitions at the U.S. Department of Energy legacy uranium ore processing site in Riverton, WY, through spring-summer-fall hydrological transitions. Our goal was to characterize the microbial community throughout the soil profile, down to the saturated aquifer, and observe its response to wet-dry transitions across a full season and compare to changes in geochemistry and hydrology. Next-generation sequencing was employed to identify biogeochemically-relevant microbial taxa based on the 16S rRNA gene; we found a broad diversity of microbial clades including taxa involved in sulfur and metal cycling, as well as nitrification. These data were paired with measurements of soil moisture, major nutrients and cations, and trace elements. Overall microbial community composition was dependent on soil depth or type, with seasonal effects only observed in the topsoil or subsurface aquifer. This finding indicates that microbial communities in the transiently-reduced center of the soil profile at the Riverton, WY site are remarkably stable, despite moisture and redox inversions. In addition, these communities likely impact the communities in surrounding soil horizons through export of metabolites and solutes as the water table rises and falls throughout the season.

16S rRNA↗

NASA NTRS2008

NASA Tech Briefs, June 2008

Topics covered include: Charge-Control Unit for Testing Lithium-Ion Cells; Measuring Positions of Objects Using Two or More Cameras; Lidar System for Airborne Measurement of Clouds and Aerosols; Radiation-Insensitive Inverse Majority Gates; Reduced-Order Kalman Filtering for Processing Relative Measurements; Spaceborne Processor Array; Instrumentation System Diagnoses a Thermocouple; Chromatic Modulator for a High-Resolution CCD or APS; Commercial Product Activation Using RFID; Cup Cylindrical Waveguide Antenna; Aerobraking Maneuver (ABM) Report Generator; ABM Drag_Pass Report Generator; Transformation of OODT CAS to Perform Larger Tasks; Visualization Component of Vehicle Health Decision Support System; Mars Reconnaissance Orbiter Uplink Analysis Tool; Problem Reporting System; G-Guidance Interface Design for Small Body Mission Simulation; DSN Scheduling Engine; Replacement Sequence of Events Generator; Force-Control Algorithm for Surface Sampling; Tool for Merging Proposals Into DSN Schedules; Micromachined Slits for Imaging Spectrometers; Fabricating Nanodots Using Lift-Off of a Nanopore Template; Making Complex Electrically Conductive Patterns on Cloth; Special Polymer/Carbon Composite Films for Detecting SO2; Nickel-Based Superalloy Resists Embrittlement by Hydrogen; Chemical Passivation of Li+-Conducting Solid Electrolytes; Organic/Inorganic Polymeric Composites for Heat-Transfer Reduction; Composite Cathodes for Dual-Rate Li-Ion Batteries; Improved Descent-Rate Limiting Mechanism; Alignment-Insensitive Lower-Cost Telescope Architecture; Micro-Resistojet for Small Satellites; Using Piezoelectric Devices to Transmit Power through Walls; Miniature Latching Valve; Apparatus for Sampling Surface Contamination; Novel Species of Non-Spore-Forming Bacteria; Chamber for Aerosol Deposition of Bioparticles; Hyperspectral Sun Photometer for Atmospheric Characterization and Vicarious Calibrations; Dynamic Stability and Gravitational Balancing of Multiple Extended Bodies; Simulation of Stochastic Processes by Coupled ODE-PDE; Cluster Inter-Spacecraft Communications; Genetic Algorithm Optimizes Q-LAW Control Parameters; Low-Impact Mating System for Docking Spacecraft; Non-Destructive Evaluation of Materials via Ultraviolet Spectroscopy; Gold-on-Polymer-Based Sensing Films for Detection of Organic and Inorganic Analytes in the Air; and Quantum-Inspired Maximizer.

Source record↗

NASA NTRS2011

Post-Fragmentation Whole Genome Amplification-Based Method

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Benardini, James↗

DOE OSTI2021

JGI QC impact on assembly, binning, phylogenomics, and functional analysis

Background Investigators using metagenomic sequencing to study their microbiomes are often provided data that has been trimmed and decontaminated or do it themselves without knowing the effect these procedures can have on their downstream analyses. Here we evaluated the impact that JGI trimming and decontamination procedures had on assembly and binning metrics, placement of metagenome assembled genomes into species trees, and functional profiles of metagenome-assembled genomes (MAGs) extracted from twenty three complex rhizosphere metagenomes. We also investigated how more aggressive trimming impacts these binning metrics. Results We found that JGI trimmed and decontamination of input reads had some significant impacts in assembly and binning metrics compared to raw reads, and that differences in placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. More aggressive trimming beyond those used by JGI were found to reduce MAG counts. Conclusions Mild trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing? However, mild trimming and decontamination of metagenomic reads with high quality scores is recommended for those who elect to do so.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Impact of BBDuk metagenomic read trimming and decontamination

59 BASIC BIOLOGICAL SCIENCES↗