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At least 775 records · Page 43

Genetic Determinants of Microbial Survival in Space

Space flight agencies envision a future for humankind beyond Earth, including missions back to the Moon and to Mars in the coming decades. Sending humans into space inevitably includes their microbiomes as well, leading to trillions of bacteria being shed in their living areas. These bacteria shape the lives of their hosts as well as their environment; thus, it is crucial to understand the adaptations of these microbial spacefarers in spaceflight conditions. We aimed to elucidate the genetic determinants of microbial survival in space using a pan-genome analysis of 12 genera cultured from the International Space Station (ISS) from 2017 to 2018. Analysis was performed on each of the genera individually with terrestrial analogs to identify the core and accessory genomes of the spaceflight and terrestrial strains. We then compared the flight and terrestrial core and accessory genomes for each genera using a Bray-Curtis index and visualized the resulting dissimilarity using an Non-Metric Dimensional Scaling plot. The core proteins available in only the spaceflight organisms were then manually characterized for function and genomic location. In every core genome comparison in each genus, there was significant dissimilarity in the core of the spaceflight organisms when compared to the terrestrial organisms. This trend was present in some of the accessory genomes, but was not ubiquitous. Functional analysis of the core content of the ISS genomes showed the majority of genes unique to the core were clustered by location. These gene clusters suggested a set of genetic determinants confer survival in spacecraft-built environments, notably through the uptake of extracellular DNA such as bacteriophage and plasmids. The clear difference between spaceflight and terrestrial microorganisms shows that spaceflight conditions are selective, which has long term implications for their human hosts and environments.

MoBE↗

Preparation for and Performance of a Pseudomonas aeruginosa Biofilm Experiment On Board the International Space Station

Biofilms are a problem on Earth given their ability to degrade the materials upon which they grow and due to their relevance to infections. Remarkably, 65% and 80% of infections and chronic diseases on Earth are associated with biofilms, respectively. In space, these problems' impact is higher because the crew's lives and mission success depend on nominal operation of mechanical systems. Furthermore, the isolated confined environment nature of spaceflight may increase the rates of disease transmission. In the case of the International Space Station (ISS), biofilms are an identified problem on the Environmental Control and Life Support System (ECLSS), namely on the water processor assembly (WPA). In late 2019, the Space Biofilms experiment launched towards ISS to (i) characterize the mass, thickness, morphology, and gene expression of biofilms formed in space with respect to matched Earth controls, (ii) interrogate the expression of antimicrobial resistance genes, and (iii) test novel materials as potential biofilm control strategies for future ECLSS components. For this, 288 bacterial samples were prepared prior to the launch of the Northrop Grumman CRS-12 mission from NASA's Wallops Flight Facility. The samples were integrated into the spaceflight hardware, BioServe's Fluid Processing Apparatus (FPA) packed in sets of eight in Group Activation Packs (GAP). Half of these samples were activated and terminated on orbit by NASA astronauts Jessica Meir and Christina Koch, while the remaining half were processed equivalently on Earth. The spaceflight bacterial samples of Space Biofilms returned on board SpaceX' CRS-19 Dragon spacecraft, in early 2020. We here describe the test campaign implemented to verify the experiment design and confirm it would enable us to achieve the project's scientific goals. This campaign ended with the Experiment Verification Test (EVT), from which we here present example morphology and transcriptomic results. We describe in detail the sample preparation prior to flight, including cleaning and sterilization of the coupons of six materials (SS316, passivated-SS316, lubricant impregnated surface, catheter-grade silicone with and without a nanotopography, and cellulose membrane), loading and integration of growth media, bacterial inoculum, fixative and preservative to enable experiment termination on orbit. Additionally, we describe the performance of the experiment on board the ISS, including crew activities, use of assets, temperature profile, and experiment timeline; all leading to a successful spaceflight experiment.

Pamela Flores↗

Oncogenic Integration of Nucleotide Metabolism via Fatty Acid Synthase in Non-Hodgkin Lymphoma

Metabolic dysfunctions enabling increased nucleotide biosynthesis are necessary for supporting malignant proliferation. Our investigations indicate that upregulation of fatty acid synthase (FASN) and de novo lipogenesis, commonly observed in many cancers, are associated with nucleotide metabolic dysfunction in lymphoma. The results from our experiments showed that ribonucleotide and deoxyribonucleotide pool depletion, suppression of global RNA/DNA synthesis, and cell cycle inhibition occurred in the presence of FASN inhibition. Subsequently, we observed that FASN inhibition caused metabolic blockade in the rate-limiting step of the oxidative branch of the pentose phosphate pathway (oxPPP) catalyzed by phosphogluconate dehydrogenase (PGDH). Furthermore, we determined that FASN inhibitor treatment resulted in NADPH accumulation and inhibition of PGDH enzyme activity. NADPH is a cofactor utilized by FASN, also a known allosteric inhibitor of PGDH. Through cell-free enzyme assays consisting of FASN and PGDH, we delineated that the PGDH-catalyzed ribulose-5-phosphate synthesis is enhanced in the presence of FASN and is suppressed by increasing concentrations of NADPH. Additionally, we observed that FASN and PGDH were colocalized in the cytosol. The results from these experiments led us to conclude that NADP–NADPH turnover and the reciprocal stimulation of FASN and PGDH catalysis are involved in promoting oxPPP and nucleotide biosynthesis in lymphoma. Finally, a transcriptomic analysis of non-Hodgkin’s lymphoma (n = 624) revealed the increased expression of genes associated with metabolic functions interlinked with oxPPP, while the expression of genes participating in oxPPP remained unaltered. Together we conclude that FASN–PGDH enzymatic interactions are involved in enabling oxPPP and nucleotide metabolic dysfunction in lymphoma tumors.

Non-Hodgkin lymphoma↗

The Light Microscopy Module A Facility Overview-History and Science

We will share a brief history and provide a science overview of the many accomplishments of the Light Microscopy Module (LMM), a microscope that has been operating in the microgravity environment of the International Space Station (ISS) since 2010. It will be removed in October 2021. It was initially outfitted for the Constrained Vapor Bubble – Wickless Heat Pipe experiment. It was later reconfigured and upgraded many times to support a broad portfolio of Physical science and Biological experiments including: Complex Fluids, Colloids, Macro-Molecular Biophysics, Protein Crystals, and Plant Biology. The LMM has enabled many significant studies and discoveries and has seen its fair share of pleasant surprises. These include recording order arising out of disorder, e.g., systems of colloids that were glasses on Earth crystallizing to form large defect-free crystals, nematic ordering of elliptical colloids, and colloidal-polymer systems crystallizing. The LMM science teams have also seen how to improve product stabilizers once the effects of sedimentation on Earth were removed; they were able to see which tagged genes express in plants when gravity is removed, telling them which genes are essential for growing plants in space; they’ve tested protein crystal growth models; checked models for creating bijel electrodes that turn batteries into fast-charging supercapacitors; tested many forms of colloidal self-assembly: including those using depletion attraction, magnetic fields, and critical Casimir forces; they’ve observed explosive bubble nucleation in a wickless heat pipe, and much more. This work has been supported by the NASA Biological and Physical Sciences (BPS) Division and the ISS Program Office, Johnson Space Center Code OZ and Code OB, the Center for the Advancement of Science in Space (CASIS) / ISS National Lab, EPSCoR, and ISS international partners from ESA – the Netherlands and Italy, CSA, JAXA and S. Korea, and by Space Act Agreements with Procter and Gamble (P&G).

Colloids↗

Adaptation to environmental extremes structures functional traits in biological soil crust and hypolithic microbial communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semi-translucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities waging war using the Type VI Secretion System (T6SS) and hypoliths favoring diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

Biological soil crusts↗

Development of Computational Environmental Microbiome Workflows for the Laboratory and the International Space Station

Identification of microorganisms in the spaceflight environment is critical for crew health risk assessment on the International Space Station (ISS). Since 2017, nanopore sequencing technology has been used to support thein situ identification of microbial species during spaceflight. Beginning in 2018, a culture-independent, swab-to-sequencer method was implemented onboard the ISS to provide a more thorough insight of the ISS microbiome. Eliminating microbial culture enables identification of difficult-to-culture organisms, reduces risks associated with potentially pathogenic cultures, and could significantly reduce the time from sample-to-answer. However, this molecular-based approach generates large metagenomic datasets that require substantial computational resources for analysis. To process nanopore-generated sequencing data, the JSC Microbiology Laboratory established a bioinformatics workflow on Amazon EC2 under the security guidance of the NASA Science Managed Cloud Environment (SMCE).This resource allows for the development, testing, and accessing of computational tools for processing large and complex datasets. The work described here will address the downlinking of data from the ISS, the automated pipeline developed to identify targeted bacterial and fungal organisms, and the time from sampling onboard to microbial identification. The pipelines have been enhanced to address high and low biomass samples using optimization based on sample source (air, water, or surface) and type of collection (filter, colony, or swab).The resulting microbiome data can be assessed beyond microbial identifications to gain understanding toward population changes over time, potential selective environmental pressures, and evaluating correlations with a wide range of additional data sets. Metagenome analysis pipelines in development could allow for simultaneous identification of microbial species, gene function, and gene pathways present in the environment. Beyond the ground processing, the developed analysis pipeline is currently deployed onboard the ISS to allow for near real-time assessments of the ISS microbiome. This study serves as a critical foundation for exploration missions, where rapid microbiome analyses will be required.

G. Marie Sharp↗

Microbial Monitoring of New Cleanrooms Used to Curate Astrobiologically Relevant Asteroid Samples from Bennu and Ryugu

Introduction: NASA has constructed two new cleanrooms to house materials from the OSRIS-REx and Hayabusa2 missions to the asteroids Ryugu (162173) and Bennu (101955), respectively. In accordance with standard astromaterials curation practices, these cleanrooms will be monitored for particulate contamination and maintained to ISO 5 equivalent standards1. Since the samples in these collections are expected to contain prebiotic organic compounds that may help explain the origin of life on Earth, these labs will also be monitored for organic and biological contamination2. Samples from Ryugu arrived on Earth in December, 2020. After basic characterization in Japan, NASA received a subset of these samples at the astromaterials curation facility in Houston in December of 2021. OSIRIS-REx is expected to return samples in September, 2023. Here we present preliminary microbial monitoring results from monthly monitoring of these new labs and the connected microtomy and staging areas that support them, as they are being commissioned. We also compare these results to baseline values for other astromaterials curation labs. We will also briefly describe additional cleaning efforts employed to reduce the bioburden in these new cleanrooms. Methods: Microbial samples were collected from surfaces using a dry macrofoam swab (Puritan Brand 2518051PFRNDFD). Swabs were also opened in the lab but not touched to any surfaces to function as negative controls. Samples and controls were processed inside a class II biosafety cabinet to avoid inadvertent cross contamination. The swabs were suspended in 15 ml of PBS (Phosphate Buffered Saline) and vortexed for 20 seconds to remove cells from the swab surface. The PBS was used to inoculate Petri dishes filled with TSA (Tryptic Soy Agar), Blood Agar, or Reasoners 2 agar to check for microbial growth. Each plate was inoculated with 0.1 ml of PBS. The TSA and blood agar plates were incubated at 35˚C and the Reasoners 2 agar plates were incubated at 25˚C for seven days. Petri dishes filled with Potato dextrose agar, Saboraud dextrose agar, or Saboraud dextrose agar with 0.1 mg/ml of chloramphenicol, an antibiotic, were used to check for fungal growth. These plates were inoculated with 0.3 ml of PBS and incubated at 30˚C. The remaining PBS was frozen at -80 ˚C for DNA sequencing. After incubation, isolates were counted and reisolated for identification. Isolates were identified using the VITEK23 system or by sequencing a portion of the 16S rRNA gene for bacteria or the ribosomal internal transcribed spacer (ITS) for fungi. Sequencing was performed with an ABI 3500 Sanger sequencer. Results: During our initial sampling, six of the seven sites sampled (86%) displayed bacterial or fungal growth. Samples collected from the staging areas and microtomy labs are not included in this calculation since those areas are maintained at a lower ISO 7 equivalent cleanliness standard. A month later, only three of the seven sites (43%) displayed bacterial growth. No fungal growth was detected in the second sampling. Since new equipment had been introduced to the Hayabusa2 lab since the first round of sampling, an additional three sampling sites were included in the second round of sampling. None of these sites displayed microbial growth. These sites will be included in all future sampling efforts. Bacterial isolates have been identified from the following genera at multiple time points: Micrococcus, Staphylococcus, and Bacillus. Isolates from the genera: Microbacterium, Nocardioides, Methylocystis, and Microvirga were identified in the initial sampling, but were not present at later time points. Identification of fungal isolates is in progress. Results are summarized in Table 1. Discussion: The recovery rate or percentage of positive samples4 was initially 86%, which is higher than the median recovery rate for comparable ISO 5 equivalent curation labs like Stardust (33%), Hayabusa (33%), and Cosmic Dust (50%). However, after a month of operation, the recovery rate for these same sites decreased to 43%, which is similar to what we observe in comparable curation cleanrooms with no microbial control requirements. Adding in the new sampling sites further decreases the recovery rate to 30%. With the reduction in recovery rate, we also observed a decrease in microbial diversity. At the first time point, we observed at least 10 different bacterial species and at least two different fungi. This is a higher diversity than the median values for comparable ISO 5 equivalent labs (2-4 isolates per sampling event). After the second sampling, we observed at least 4 bacterial species and no fungi, which is more consistent with comparable labs. We expect the recovery rate and diversity in both labs to continue to decrease as routine operation continues. We will use ultrapure hydrogen peroxide to disinfect equipment and work areas prior to opening any sample containers. Most of the bacterial and fungal isolates were detected on samples from the cleanroom floors. This is consistent with baseline results from other curation labs. Organisms from the genera Bacillus, Staphylococcus, and Micrococcus that were repeatedly detected are common in cleanrooms and on human skin5,6. These organisms are generally thought to be introduced when people enter the cleanroom. Microbacterium, Nocardioides, and Microvirga have also previously been identified in astromaterials cleanrooms, but not as frequently as Bacillus, Staphylococcus, and Micrococcus. Methylocystis is a novel genus in the astromaterials cleanrooms, but it was identified with low accuracy (93% match in the sequenced region of the 16S rRNA gene) and further work is needed to confirm this identification. Microbacterium is a diverse genus with isolates identified from terrestrial and aquatic sediments. Some species of Microbacterium are capable of degrading complex organic compounds found in crude oil. The presence of these bacteria in the OSIRIS REx and Hayabusa2 cleanrooms should be closely monitored. Methylocystis is a genus of methanotrophic bacteria capable of oxidizing methane. If this identification proves to be correct and it is detected again, it should be closely monitored as well. Under nominal operating conditions, samples should not ever encounter the cleanroom floor or other high traffic areas. If we observe an increase in the bioburden in sensitive work areas that appears to be influenced by organism transfer from high traffic areas like the floors, we can employ additional hydrogen peroxide treatments to disinfect high traffic areas. Routine microbial monitoring of these labs will ensure that NASA’s astromaterials collections remain pristine and useful for scientific study. Table 1. Sampling Locations and Colony Counts Bacterial CFUa Fungal CFU Bacterial CFU Fungal CFU Lab - Location 11/2/2021 11/2/2021 12/13/2021 12/13/2021 H2b-Floor 4 8 1 0 H2-staging pass through 3 0 0 0 H2-microtomy pass through TNTCc 0 0 0 H2 Microscope 1 NA NA 0 0 H2 Microscope 2 NA NA 0 0 H2-Table NA NA 0 0 OREXd- microtomy pass through 0 0 6 0 OREX – Anteroom pass through 0 0 0 0 OREX – Floor 1 2 0 0 OREX Witness Foil Table 3 0 1 0 Staging-Floor 16 0 15 0 Microtomy-Floor 3 0 2 0 a: CFU = Colony Forming Unit b: H2 = Hayabusa2 Lab c: TNTC = too numerous to count d: OREX = OSIRIS-REx Lab References: 1. ISO 14644-1:2015 - Cleanrooms and associated controlled environments -- Part 1: Classification of air cleanliness by particle concentration. 37 (2015). 2. McCubbin, F. M. et al. Space Sci Rev 215, (2019). 3. Pincus, D. H. Encyclopedia of Rapid Microbiological Methods (2005). 4. The United States Pharmacopeial Convention. USP General Chapter <1116> 17, 784–794 (2013). 5. Sheraba, N. S., Yassin, A. S. & Amin, M. BMC Research Notes 3, 278 (2010). 6. Utescher, C. L. de A., Franzolin, M. R., Trabulsi, L. R. & Gambale, V. Brazilian Journal of Microbiology 38, 710–716 (2007).

A B Regberg↗

Conserved Function of RNA Binding Motif Protein48 (RBM48) and Armadillo Repeat Containing 7 (ARMC7) in Maize and Human U12 Splicing

Splicing of pre-mRNA is fundamental for genes containing introns. Emerging data points to a deeply conserved role of this process in eukaryotic cell differentiation and proliferation. The vast majority of introns termed U2-type introns are spliced by a major spliceosome; however, there also exist rare and more conserved U12-type introns that are spliced by a minor spliceosome. Mutations that disrupt U12 splicing inhibit cell differentiation in both maize endosperm and human blood cells. However, the mechanism underlying this process is not well understood. The maize RNA Binding Motif Protein 48 (RBM48) plays an essential role as a U12 splicing factor and is required for proper maize kernel development. Using human cell lines, CRISPR-Cas9 knockdown of RBM48 demonstrated a conserved function in human U12 intron splicing. RBM48 and Armadillo Repeat Containing 7 (ARMC7) protein interact in both maize and human as part of the activated minor spliceosome. Here we show RBM48 and ARMC7 co-localization in the nucleus of human cell lines. Vertebrate ARMC7 is normally localized in the cytosol, whereas RBM48 is found in the nucleus. Our data suggests that the interaction plays a role in regulating ARMC7 localization or the efficiency of U12 intron splicing. We also performed comprehensive transcriptome profiling and identified a common subset of conserved Minor Intron Containing Genes (MIGs) impacted in both human and maize RBM48 knockout mutants. Of importance, the vast majority of these MIGs are associated with developmental defects in both plants and animals. This suggests that aberrant splicing of these targets has a high likelihood of mediating abnormal cell phenotypes. These data support evolutionarily conserved U12 splicing mechanisms between maize and humans with both RBM48 and ARMC7 having roles in the activated spliceosome.

maize↗

Tracing the Path of Carbon Export in the Ocean though DNA Sequencing of Individual Sinking Particles

Surface phytoplankton communities were linked with the carbon they export into the deep ocean by comparing 18 S rRNA gene sequence communities from surface seawater and individually isolated sinking particles. Particles were collected in sediment traps deployed at locations in the North Pacific subtropical gyre and the California Current. DNA was isolated from individual particles, bulk-collected trap particles, and the surface seawater. The relative sequence abundance of exported phytoplankton taxa in the surface water varied across functional groups and ecosystems. Of the sequences detected in sinking particles, about half were present in large (>300 μm), individually isolated particles and primarily belonged to taxa with small cell sizes (<50 μm). Exported phytoplankton taxa detected only in bulk trap samples, and thus presumably packaged in the smaller sinking size fraction, contained taxa that typically have large cell sizes (>500 m). The effect of particle degradation on the detectable 18 S rRNA gene community differed across taxa, and differences in community composition among individual particles from the same location largely reflected differences in relative degradation state. Using these data and particle imaging, we present an approach that incorporates genetic diversity into mechanistic models of the ocean's biological carbon pump, which will lead to better quantification of the ocean’s carbon cycle.

Carbon Expert↗

Discovery of Chlorophyll d : Isolation and Characterization of a Far-Red Cyanobacterium from the Original Site of Manning and Strain (1943) at Moss Beach, California

We have isolated a chlorophyll-d-containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium’s environmental description, culturing procedure, pigment composition, ultrastructure, and full genome sequence. Among cultures of far-red cyanobacteria obtained from red algae from the same site, this strain was an epiphyte on a brown macroalgae. Its Q y in vivo absorbance peak is centered at 704–705 nm, the shortest wavelength observed thus far among the various known Acaryochloris strains. Its Chl a /Chl d ratio was 0.01, with Chl d accounting for 99% of the total Chl d and Chl a mass. TEM imagery indicates the absence of phycobilisomes, corroborated by both pigment spectra and genome analysis. The Moss Beach strain codes for only a single set of genes for producing allophycocyanin. Genomic sequencing yielded a 7.25 Mbp circular chromosome and 10 circular plasmids ranging from 16 kbp to 394 kbp. We have determined that this strain shares high similarity with strain S15, an epiphyte of red algae, while its distinct gene complement and ecological niche suggest that this strain could be the closest known relative to the original Chl d source of Manning and Strain (1943). The Moss Beach strain is designated Acaryochloris sp. (marina) strain Moss Beach.

chlorophyll d↗

Prokaryotic and Fungal Characterization of the Facilities Used to Assemble, Test, and Launch the OSIRIS-REx Spacecraft

To characterize the ATLO (Assembly, Test, and Launch Operations) environment of the OSIRIS-REx spacecraft, we analyzed 17 aluminum witness foils and two blanks for bacterial, archaeal, fungal, and arthropod DNA. Under NASA’s Planetary Protection guidelines, OSIRIS-REx is a Category II outbound, Category V unrestricted sample return mission. As a result, it has no bioburden restrictions. However, the mission does have strict organic contamination requirements to achieve its primary objective of returning pristine carbonaceous asteroid regolith to Earth. Its target, near-Earth asteroid (101955) Bennu, is likely to contain organic compounds that are biologically available. Therefore, it is useful to understand what organisms were present during ATLO as part of the larger contamination knowledge effort—even though it is unlikely that any of the organisms will survive the multi-year deep space journey. Even though these samples of opportunity were not collected or preserved for DNA analysis, we successfully amplified bacterial and archaeal DNA (16S rRNA gene) from 16 of the 17 witness foils containing as few as 7 ± 3 cells per sample. Fungal DNA (ITS1) was detected in 12 of the 17 witness foils. Despite observing arthropods in some of the ATLO facilities, arthropod DNA (COI gene) was not detected. We observed 1,009 bacterial and archaeal sOTUs (sub-operational taxonomic units, 100% unique) and 167 fungal sOTUs across all of our samples (25–84 sOTUs per sample). The most abundant bacterial sOTU belonged to the genus Bacillus. This sOTU was present in blanks and may represent contamination during sample handling or storage. The sample collected from inside the fairing just prior to launch contained several unique bacterial and fungal sOTUs that describe previously uncharacterized potential for contamination during the final phase of ATLO. Additionally, fungal richness (number of sOTUs) negatively correlates with the number of carbon-bearing particles detected on samples. The total number of fungal sequences positively correlates with total amino acid concentration. These results demonstrate that it is possible to use samples of opportunity to characterize the microbiology of low-biomass environments while also revealing the limitations imposed by sample collection and preservation methods not specifically designed with biology in mind.

Aaron B. Regberg↗

Mining the Gravity Mutants of Arabidopsis

Gravity mutants are a valuable resource for understanding gravity perception, signaling, and response in plants. A review of 190 publications resulted in a list of 97 loci with mutations that caused a gravitropic phenotype. While all these mutants show some form of gravity phenotype, several are also generally defective in growth. After removing these nonspecific mutants, 76 loci were deemed to have true gravity mutants. The gene list was then used to create a sortable database containing key factors of gravity signaling as well as data on methodologies and the development of mutant lines. Indexing this database has allowed us to pull out trends that were not visible in individual publications. For example, mutants that are unable to rearrange starch statoliths make up a larger proportion of the described inflorescence stems mutants than any other organ. Comparing these statolith mutants across organs shows that root and inflorescence stems consistently display different phenotypes for the same class of defect. The more severe gravity defects are most commonly described in root tissue while other tissues are more likely to show only a delayed or reduced response to gravity. The experience of members of the GeneLab plant Analytics Working Group (AWG) in data visualization and gene mapping have sparked new ideas for utilizing this database. Knowledge of shared traits, mutant development, and growth can provide a new resource for the production of seed lines specialized for their response to gravity.

gravitropism↗

Space Flown Rodent Liver RNA Sequencing Data for Machine Learning in Space Biology Research

High-throughput nucleic acid sequencing (DNA-seq, RNA-seq) has become widespread in biomedical research due to the growing availability and affordability of these assays. Data analysis has been accelerated in recent years by the adoption of artificial intelligence (AI) and machine learning (ML) techniques by biomedical researchers. In space biology research, RNAseq datasets from space-flown experimental samples are critical for characterizing the gene expression aberrations associated with exposure to spaceflight stressors. However, space biological experiments tend to be very low sample size, so identifying proper AI/ML algorithms for sequencing data analysis is an ongoing challenge since these algorithms typically require large sample size. The NASA Science Mission Directorate (SMD) has started the “Benchmark Initiative for AI/ML”, focused on creating datasets meant for three main applications: 1) scientific benchmarking, which finds the best algorithm for a specific problem; 2) application benchmarking, which measures algorithm performance against a set of parameters; and 3) system benchmarking, which evaluates performance of hardware and software architecture. These scientific benchmarks consist of an AI-ready dataset and a reference implementation on a specific scientific question. In this work, we focused on generating standardized datasets to allow the scientific community to benchmark AI/ML algorithms in the domain of space biology. We present here a standardized, AI-ready, publicly available benchmark dataset for space biology RNA-seq data as a collaboration between the NASA AI4LS (Artificial Intelligence for Life Sciences) working group. and NASA’s SMD. This dataset consists of space-flown and ground control mouse liver found in the NASA GeneLab omics database. However, to amplify the small sample number (n=112 samples) for ML purposes, we employ Gaussian noise and a generative adversarial network to extend this dataset to 6,000 synthetic samples, matching the original gene expression characteristics.

James Casaletto↗

Optimizing Screening for Preventable Blindness With Head-Mounted Visual Assessment Technology

Age-related macular degeneration (AMD) is a leading cause of blindness and is diagnosed as early-stage or late-stage. Early-stage AMD is usually asymptomatic and entails pigmentary changes of the retina (Ayoub & Patel, 2009). As the disorder progresses, there are atrophic or neovascular changes that distort vision, especially the central visual field (Ayoub & Patel, 2009). There are several genetic and non-genetic risk factors for AMD and no proven therapy to slow or reverse late-stage atrophic AMD, while anti-VEGF has effectively treated late-stage neovascular AMD. Several genes of interest have also been investigated thoroughly thus far in their connection to AMD and the CFH and ARMS2 genes have shown promise in understanding the genetic basis of the disorder (Awh et al., 2013). There are other epigenetic and environmental factors as well including smoking and low antioxidant levels (Cano et al., 2010). Ongoing investigations include antioxidant supplementation and a smoking cessation regimen to reverse early-stage AMD (Cano et al., 2010). Progress in treating AMD as a disorder across its varied stages requires newer therapeutics along with a more detailed understanding of the genetic and cellular pathways of pathophysiology is needed to better counter this prevalent disorder of the eye.

age-related macular degeneration↗

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↗

Murine Host-gut Microbiota Interactions are Modulated During Spaceflight

The rodent habitat on the International Space Station has provided critical insight into the impact of spaceflight on mammalian physiology. These effects include dysfunction of carbohydrate, steroid and lipid metabolism, and immune response, as well as induction of symptoms characteristic of liver disease, insulin resistance, osteopenia and myopathy, which are anticipated to intensify over long-duration spaceflight. Although these physiological responses can involve the microbiome, the host-microorganism interactions during spaceflight are still largely unknown. NASA GeneLab curates a wide range of space research data and the current work harnesses GeneLab multi’omic data from recent Rodent Research studies to explore changes to gut microbiota during spaceflight and their associations with host physiology when compared to ground controls. Using a hybrid analysis of DNA barcoding and whole genome shotgun data, an array of bacteria, fungi and nematodes could be identified at species level, and significant differences in relative abundances associated with spaceflight. Functional prediction based on differential abundance of species and metagenome gene inventories as well as metatranscriptomic gene expression at the host-gut microbiome interface implicate microbiota interactions could contribute to spaceflight pathology. Harnessing carefully curated publicly available data, such as from Genelab, to generate multi‘omic space science discoveries can help decipher the complex host-microbiome interactions that influence both health on Earth and the feasibility of long-duration spaceflight.

Microbiome↗

Biological Oxidation of Fe(II)-Bearing Smectite by Microaerophilic Iron Oxidizer Sideroxydans lithotrophicus Using Dual Mto and Cyc2 Iron Oxidation Pathways

Fe(II) clays are common across many environments, making them a potentially significant microbial substrate, yet clays are not well established as an electron donor. Therefore, we explored whether Fe(II)-smectite supports the growth of Sideroxydans lithotrophicus ES-1, a microaerophilic Fe(II)-oxidizing bacterium (FeOB), using synthesized trioctahedral Fe(II)-smectite and 2% oxygen. S. lithotrophicus grew substantially and can oxidize Fe(II)-smectite to a higher extent than abiotic oxidation, based on X-ray near-edge spectroscopy (XANES). Sequential extraction showed that edge-Fe(II) is oxidized before interior-Fe(II) in both biotic and abiotic experiments. The resulting Fe(III) remains in smectite, as secondary minerals were not detected in biotic and abiotic oxidation products by XANES and Mössbauer spectroscopy. To determine the genes involved, we compared S. lithotrophicus grown on smectite versus Fe(II)-citrate using reverse-transcription quantitative PCR and found that cyc2 genes were highly expressed on both substrates, while mtoA was upregulated on smectite. Proteomics confirmed that Mto proteins were only expressed on smectite, indicating that ES-1 uses the Mto pathway to access solid Fe(II). We integrate our results into a biochemical and mineralogical model of microbial smectite oxidation. This work increases the known substrates for FeOB growth and expands the mechanisms of Fe(II)-smectite alteration in the environment.

smectite↗

Nanopore Sequencing in Space: The Advancement of In Situ Microbiome Analysis for the International Space Station and Beyond

Introduction: Routine assessment of the International Space Station (ISS) microbiome has been performed through in-flight culture and Earth-based analysis. Through utilization of the ISS, significant progress toward in situ microbial identification has been achieved. In 2016, the molecular space age began when DNA-based, Earth-prepared samples were amplified within miniPCR (Genes in Space-1), and subsequent samples were sequenced with the MinION (Biomolecule Sequencer). The following year, these platforms were used collectively to yield the first off-Earth identification of unknown bacteria collected and cultured onboard the ISS (Genes in Space-3). Further advancement occurred in 2018 when a culture-independent, direct swab-to-sequencer method revealed a more thorough depiction of the ISS surface microbiome (BEST). As NASA looks towards Artemis and extended exploration missions, it is critical to continue to harness the ISS to expand in situ nanopore sequencing-based analysis in support of microbial-related crew health, planetary protection, and space research initiatives.

Christian G. Mena↗