Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
SEARCH · Engineering Papers
Results for “SnP”
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.
Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources
Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.
59 BASIC BIOLOGICAL SCIENCES↗
WEST Diversity Panel GBS information (Ferguson et al., 2020)
Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 2020) DOI:10.1101/2020.11.02.365213.
09 BIOMASS FUELS↗
Early Progress Toward the Feasibility of the Centrifugal Nuclear Thermal Rocket
The Centrifugal Nuclear Thermal Rocket (CNTR) is a Nuclear Thermal Propulsion (NTP) concept designed to heat propellant directly by the reactor fuel. The primary difference between the CNTR concept and traditional NTP systems is that rather than using traditional solid fuel elements, the CNTR uses liquid fuel with the liquid contained in rotating cylinders by centrifugal force. If the concept can be successfully realized, the CNTR would have a high specific impulse (~1800 seconds) at high thrust, which may enable (i) viable near-term human Mars exploration by reducing round-trip times to 420 days and (ii) direct injection orbits for scientific missions to the Solar System outer planets and potentially Kuiper Belt objects. The CNTR could also use storable propellants such as ammonia, methane, or hydrazine at an Isp of ~900 seconds, enabling long-term in-space storage of a dormant system. Significant engineering challenges must be addressed to establish the technical viability of the CNTR. Research is presently underway to determine resolutions for these engineering challenges. In particular, research has begun on the analytical modeling and simulation of the two-phase heat transfer between the liquid metallic uranium fuel and the gaseous propellant. A paper was presented at the 2021 IAC which described these challenges and the study plan to address them. This paper describes the analytical and experimental progress to date toward resolving these challenges and establishing the engineering feasibility of the CNTR technology
High Performance Nuclear Thermal Propulsion NTP SN↗
Testing Capabilities and Needs for Fission Space Nuclear Systems-Engine Ground Testing
Explore the source record for details and available documents.
NTP↗
Nuclear Thermal Propulsion (NTP) - Propelling into the Future
Nuclear Thermal Propulsion (NTP) is the exciting advancement of engine system technology that will enable NASA to perform deep space missions previously beyond reach. Since the 1940s, the United States has attempted to mature this technology to fulfill the mission that JFK famously declared in his special address to Congress in 1961 stating our need to “Accelerate development of the Rover nuclear rocket. This gives promise of someday providing a means for even more exciting and ambitious exploration of space… to the very end of the solar system itself.” Today, we are dedicated to realize this mission, embarking on the journey with other government agencies and industry giants to boldly go where no one has gone before…
NTP↗
Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations
The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.
Biology↗
Developing a Genetic Variant Calling Pipeline for Quantifying the Complex Mutagenic Load Accumulated in BioNutrients-1 Production Pack Samples
Microorganisms hold great promise for on demand production of labile nutrients and pharmaceuticals as well recycling and in situ resource utilization. The utilization of microorganisms for such tasks on space missions is hindered by the limited data on how microbes respond to spaceflight. For example, the genetic stability of microorganisms, and the genomic engineered traits added to deliver desired functions, over long-term storage in the spacecraft environment is poorly understood. The BioNutrients-1 (BN-1) mission conducted a 5-year study of desiccated storage in Low Earth Orbit (LEO) to evaluate the suitability of eight synthetic biology chassis organisms for long-duration space missions. We are employing high-depth, whole genome sequencing (WGS) to determine the mutagenic load that accumulated during long-term storage. Mutation analysis pipelines are well established for homogenous culture grown from a single colony, but the mutational landscape of the BN-1 samples present a unique analysis challenge, as every cell in the BN-1 samples had a unique genetic journey of DNA damage and repair. Consequently, sequence variants are expected at low allele frequency within samples. To address this genetic complexity, we apply two distinct computational approaches to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO. For reference genome free mutation detection, we utilized DiscoSNP++, which is a de Bruijn graph approach. For reference genome-based mutation detection we utilize GATK for Microbes, which is a Bayesian probabilistic approach. We will benchmark these approaches against the mutations originally identified using CRISP, a method optimized for pooled samples. Ultimately, quantifying the mutation load imposed by storage or growth on the ISS will help identify chassis organisms with both high levels of genome stability and viability, which are desirable traits for implementation of bioproduction in long-duration missions.
SNP↗
Parameterization of Nuclear Electric Propulsion Trajectories for Outer Solar System Science Missions Methodology
This manuscript addresses the methodology used to create a database of low thrust missions to outer planets. This database utilizes previous work modeling NEP systems to determine the maximum delivered mass to outer planets based on a range of mission parameters, such as time of flight, launch vehicle, and power system mass. Trajectories were selected which best utilized NEP benefits. Additionally, a discussion on the database outputs for missions to Saturn is included, such as time of flight based on trajectory type and maximum payload, given a specific launch vehicle. The purpose of this work was to create a basis for future mission design, and a tool to investigate general trends across mission options.
Outer Planets↗