DNA sequencing provides a wealth of information about biological systems and is a pillar of modern science. If deployed to space, DNA sequencing would improve our capacity to monitor astronaut health, understand the microbial populations that inhabit spacecraft, and detect extraterrestrial life. Until recently, DNA sequencers were large and challenging to run, making their operation in space prohibitive. Nanopore DNA sequencers detect changes in conductivity as DNA bases pass through pores with diameters of ~1 nm and can be dramatically smaller and simpler to operate. This study tests the operation of the Oxford Nanopore MinION DNA sequencer on the International Space Station (ISS) and is the first demonstration of DNA sequencing in space. Multiple samples containing mixtures of DNA from Enterobacteria phage lambda, Escherichia coli and Mus musculus were sequenced with MinION sequencers on the ISS and on the ground using matched conditions. The same DNA mixtures were also sequenced with more traditional technologies (PacBio RSII, Illumina MiSeq) to allow comparison.
This work was funded in part by the NASA International Space Station program office; the NASA Postdoctoral Program; Starr Cancer Consortium grant I9-A9-071; the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts; the Bert L and N Kuggie Vallee Foundation; the WorldQuant Foundation; the Pershing Square Sohn Cancer Research Alliance; NASA grants NNX14AH50G and 15Omni2-0063; National Institutes of Health grants R25EB020393, R01ES021006 and R21AI120977; Bill and Melinda Gates Foundation grant OPP1151054; Alfred P. Sloan Foundation grant G-2015-13964; the California Initiative to Advance Precision Medicine; and Abbott Laboratories, Inc.
The microbes that colonize the surfaces of the International Space Station hitch a ride there from earth on astronauts, supplies or hardware. Regular cleaning removes many microbes, and the ones that persist may be resistant to the cleaning regimens. Understanding how the constellation of microbes on the surfaces of the International Space Station changes over time is important to reduce potential health hazards to the crew, as well as to determine how to best preserve the structural integrity of the spaceship. This study sampled heavily used surfaces of the ISS Kibo module including the incubator, air intake and handrail over three missions.
This study was supported by JAXA.
Robust microbial growth occurs in a fairly narrow range of pressures, but many bacteria can survive exposures to low pressure. This experiment explored how Bacillus subtilis respond to a low pressure of 5 kPa, such as might be encountered in the upper atmosphere at an altitude of 20 km (Mars atmosphere <1 kPa). This study will help reveal the cellular responses that are affected by exposure of B. subtilis to low pressure.
This work was funded in part by grants from the NASA Astrobiology: Exobiology and Evolutionary Biology program (NNX08AO15G); the NASA Planetary Biology Internship (PBI) program, and the NASA Earth and Space Science Fellowship (NESSF) program (13-PLANET13F-0084)
Exposure to Galactic Cosmic Radiation (GCR) presents a significant health risk to astronauts on long-duration missions beyond low Earth orbit. The researchers studied the impact of a particular form of radiation called high-mass, high-charged (HZE) particles which come in many forms. In Space, these high-energy HZE particles originate from exploding stars and are propelled through space at high speeds. HZE particles can penetrate solid objects such as the protective shielding of space vehicles, and cause significant cellular damage. In this ground-based study, human bronchial epithelial cells were exposed to HZE particles composed of either iron or silicon isotopes of varying energies, as well as to lower energy gamma rays. Cellular survival was determined and transcriptional profiling by microarray analysis was carried out at four time-points within the 24 hours following radiation exposure. This study will also aid in the assessment of HZE radiation treatment as a cancer therapy.
This work was supported by NASA NSCOR NNJ05HD36G and NNX11AC54G; Lung Cancer Spore P50 CA70907; Cancer Center Support Grant P30 CA142543
Breast cancer is one of the most common cancers associated with radiation exposure. Cosmic radiation exposure during long duration spaceflight carries uncharacterized risks. This experiment sought to understand how radiation exposure to high-energy HZE particles, that might be experienced during spaceflight beyond low earth orbit, affects mammary tumor development compared to lower energy gamma-radiation exposure commonly encountered on Earth. The researchers implanted mammary tumor cells into mice that had previously undergone exposure to radiation varying in energy and dose including densely ionizing silicon particles, lower energy gamma-radiation, or control sham-irradiation. Thus the effect of the environment on tumor progression was studied. Tumors were analyzed for global gene expression using microarray analysis and characterized histologically for molecular markers indicative of tumor stage. The study indicated that more aggressive tumors formed in animals exposed to densely ionizing particles.
This competitively selected study was funded by the NASA Space Radiation Program NSCOR award to Mary Helen Barcellos-Hoff (NASA Taskbook Grant NNX09AM52G)
Children exposed to ionizing radiation have a substantially greater breast cancer risk than adults exposed to ionizing radiation. To distinguish between several models for how exposure as a child increases the risk, this study used a mouse model and compared breast tissue in animals exposed as juveniles to ionizing radiation, gamma irradiation, or a control sham irradiation. In addition to the expression microarrays available here, the researchers developed in silico models to distinguish between various hypotheses. The researchers conclude that irradiation during puberty transiently increases stem cell self-renewal, which increases susceptibility to developing breast cancer.
This competitively selected study was funded by the NASA Space Radiation Program Specialized Center for Research in Radiation Health Effects (NSCOR) award to Mary Helen Barcellos-Hoff (NASA Taskbook Grant NNX09AM52G) and by the DOE Low-Dose Radiation program
Ionizing radiation, such as astronauts would encounter on missions beyond low-Earth orbit, is a well-established carcinogen in rodent models and a risk factor associated with human cancer. This study was designed to tease out the effects of ionizing radiation on the cells that support and influence a tumor's growth and malignancy, versus the effects on the tumor itself. The researchers implanted non-irradiated tumor tissue into mice that had been previously irradiated with ionizing radiation, lower energy gamma-rays or sham irradiated and then followed tumor development. More aggressive tumors were formed in mice exposed to ionizing irradiation prior to tumor implantation. The datasets presented here represent the expression profiles of the tumors in each of the different host environments. The results have implications in understanding tumor etiology and assessing tumor risk in individuals who have been previously exposed to ionizing radiation.
This competitively selected study was funded by the NASA Space Radiation Program Specialized Center for Research in Radiation Health Effects (NSCOR) award to Mary Helen Barcellos-Hoff (NASA Taskbook Grant NNX09AM52G) and the Department of Energy, Office of Biological and Environmental Research program on Low-Dose Radiation. Additional funding was provided from the NCI Breast SPORE program P50-CA58223, by RO1-CA138255 and RO1-CA148761, and by the Breast Cancer Research Foundation.
Most breast cancers are carcinomas that arise from the mammary epithelium. Astronauts are exposed to higher levels of ionizing radiation (IR), which is the most firmly established environmental cause of human breast cancer in both women and men. IR is also used as a cancer treatment. This study investigated the combined effect on cultured human mammary epithelial cells of exposure to IR and to the cytokine transforming growth factor beta1 (TGFbeta). TGFbeta plays a very complicated role in breast cancer; it suppresses tumor growth during the initial stage of tumorigenesis, but can switch to a tumor promoter as the stage of the tumor progresses. Gene expression was studied by transcription profiling using microarray analysis of these cells, and shows that IR causes human mammary epithelial cells to undergo an epithelial to mesenchymal transition in the presence of TGFbeta. The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells lose their characteristic shape and tight connections to one another, and gain the ability to move and invade tissues: properties of mesenchymal stem cells. Carcinoma cells undergoing an EMT may invade and metastasize and thereby generate the final, life-threatening manifestations of cancer progression.
This study was supported by a National Aeronautics and Space Administration Specialized Center for Research in Radiation Health Effects (NSCOR) award to Mary Helen Barcellos-Hoff (NASA Taskbook Grant NNX09AM52G) ; the Low Dose Radiation Program of the U.S. Department of Energy Office of Biological Effects Research; U.S. Department of Defense DAMD17-00-1-0224 (A.C. Erickson); and the Office of Health and Environmental Research, Health Effects Division, U.S. Department of Energy (contract 03-76SF00098).
Ground-based simulators of microgravity are valuable tools for preparing spaceflight experiments and cost-efficient platforms for gravitational research. The effects of clinorotation on gene expression during Zebrafish development were studied after one day of clinorotation of 5-day old free-swimming larvae. The morphological effects of clinorotation on bone and cartilage structure were studied after longer exposures of 5 days clinorotation.
This work was supported by the 'Fonds de la Recherche Fondamentale Collective', the University of Liege GAME project, the European Space Agency projects, the Belgian Space Agency Prodex projects, Netherlands Organisation for Scientific (NWO) Research Earth, and Life Sciences via the Netherlands Space Office (NSO) and ESA
Medaka or killifish are small fish that inhabit rice paddies and have the distinction of having been the first vertebrate to mate in orbit on the Space Shuttle Columbia in 1994. Medaka are model organisms to study vertebrate development and space adaptation. In a multi-investigator experiment, the response to space flight was studied in six-week-old male and female Japanese medaka that were maintained for two months in the Aquatic Habitat system on the ISS. The transcriptome of six tissues (brain, eye, ovary, testis, liver and intestine) was studied using RNA-seq analysis. Histological analysis was also conducted. Though histological analysis indicated the ovary was the only tissue that showed significant spaceflight effects, all tissues showed significant changes at the level of transcription.
This research was supported by a Grant-in-Aid for Scientific Research to Hiroshi Mitani from the Japanese Ministry of Education, Culture, Sports, Science. Additional funding was from Technology of Japan and Japan Aerospace eXploration Agency (JAXA)
RNA interference (RNAi) is a biological pathway by which RNA molecules turn down or shut off the expression of genes by directly binding to complementary RNAs and activating molecular machinery to destroy the RNA. The RNAi pathway was discovered in the nematode C. elegans, but is common in all animals including humans, and is a promising therapeutic approach for combating diseases and even viral infections on Earth. This experiment used nematodes to determine whether the RNAi pathway is functional in the spaceflight environment. Crucial functional parts of the RNAi machinery, microRNAs, as well as transcripts and protein levels of the molecular components were assayed. The authors concluded that "treatment with RNAi works as effectively in the space environment as on Earth within multiple tissues, suggesting RNAi may provide an effective tool for combating spaceflight-induced pathologies aboard future long-duration space missions. Furthermore, this is the first demonstration that RNAi can be utilized to block muscle protein degradation, both on Earth and in space" indicating promise for the use of RNAi as a therapeutic approach to combat muscle degradation in space.
This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, the Japan Society for the Promotion of Science, and Ground-Based Research Announcement for Space Utilization promoted by the Japan Space Forum. TE was supported by the Medical Research Council UK. NJS was supported by the National Institutes of Health.
Astronaut intestinal health may be impacted by microgravity, radiation, and diet. The aim of this study was to characterize how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota and colon function. Microbiota and mucosal characterization in these models is a first step in understanding the impact of the space environment on intestinal health. Three independent experiments were conducted. Experiment #1 compared four groups of rats exposed to adequate or high levels of dietary iron with or without low LET gamma radiation. In experiment #2, female mice were subjected to high LET particle exposure while suspended so that they were only partially weight-bearing. In experiment #3, the intestinal microbiota was assayed in mice that had flown for thirteen days on the Space Shuttle Atlantis.
This study was funded by the NASA Human Research Program's Human Health Countermeasures Element; a National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases grant, and a National Space Biomedical Research Institute grant.
In the future, NASA astronauts journeying into deep space may use small devices or sensors to monitor exposure to hazardous ionizing radiation. The first step in the development of such a device is to determine how the body responds to radiation in the form of biomarkers. In this study, the researchers exposed human blood to varying doses of radiation and then used microarray analysis to analyze gene expression at varying times to determine which genes could serve as biomarkers for radiation exposure.
Funding was provided by the National Aeronautics and Space Administration (NASA) contract NNX10AJ36G; the National institutes of Health (NIH) grants P20RR016481, 3P20RR016481-09S1, and P20GM103436.
A major difficulty with biological spaceflight experiments is to differentiate the response to microgravity from the other potential confounding environmental influences including such factors as suboptimal temperature or pressure. Here the authors used a suite of ground based facilities to alter gravity to tease out the transcriptional responses of fruit flies to a suboptimal environment versus the transcriptional responses to altered gravity.
This work was supported by grants from the Spanish Space Program in the “Plan Nacional de Investigacion Cientifica y Desarrollo Tecnologico” [ESP2006-13600-C02-01] and MICINN [AYA2009-07792-E]; the Dutch NWO-ALW-SRON grant [MG-057] and the UK Engineering and Physical Sciences Research Council (EPSRC), Basic Technology grants [GR/S83005/01 and EP/G037647/1]
NASA's Microbial Payload Tracking (Microbial Observatory-1) is an ongoing census of the microbial community on the International Space Station (ISS). Sampling of the surfaces and atmosphere of the ISS over time is performed by crew members. To evaluate the potential risk to fouling of clean air supplies or contamination of fluids and food, areas that crew members contact daily are targeted for sampling including the dining area, exercise equipment, lavatory, and cupola (the best view in the house). Identifying which microbes flourish in the spaceflight and microgravity environment is important from a crew health perspective given the published findings that pathogenic bacteria become more virulent in this environment. The analysis in these six new datasets was led by Dr. Kasthuri Venkateswaran at NASA's Jet Propulsion Laboratory. More information on the Microbial Observatory-1 series can be found here.
The ISS has its own environmental microbiome shaped by microgravity, radiation, and limited human presence. To determine the microbial diversity of the ISS, environmental samples were collected from several ISS surface locations from three flight opportunities. Microbe abundance was determined by 16S ribosomal RNA gene (bacteria and archaea) and ITS (fungi) sequencing. A larger goal of this study was to determine the cultivable, total, and viable microbial diversity from the collected ISS surface samples.
To further understand how the microbial diversity of the International Space Station changes over time, researchers performed sequencing studies on environmental samples taken from eight different locations on three consecutive sampling sessions. In the study, the main objective was to identify the pool of genes for each location during each sample time to understand the functional and metabolic diversity of microorganisms in the ISS. Identification of the genes was achieved by random DNA sequencing of the pooled samples and mapping to a protein database.
Tracking of antimicrobial resistance genes is crucial to understanding the risk to for infection and illness to crew working in the closed environment of the ISS. In this study, DNA extracted from each environmental sample was used to create amplicon libraries based on a customized panel of 500 antimicrobial resistance genes followed by next-generation sequencing.
BSL-2 organisms have moderate potential hazard to humans and the environment. The classification includes various microbes that cause mild disease in humans. In this study researchers isolated and characterized bacterial strains from the ISS that showed multiple drug resistance to antibiotics. Whole genome sequencing was performed for 21 strains and is provided in this investigation. Analysis of these strains could lead to further insight of the influence of microgravity on the pathogenicity and virulence of the microorganisms..
Crew-associated environmental samples were collected from the Kibo Japanese Experiment Module (JEM), US Segment Harmony Node 2, and Russian Segment Zvezda module of the International Space Station and cultured in the laboratory of Dr. Venkateswaran at the Jet Propulsion Laboratory to isolate individual bacterial species. 16S rRNA gene sequencing identified 11 Bacillus isolates belonging to a subgroup of the Bacillus genus known as the B. anthracis/B. cereus/B. thuringiensis group. Whole genome sequence of each of the 11 isolates is provided here.
The overall analysis places these strains defines a previously uncharacterized Bacillus species, now called Bacillus issensis.
As part of the ISS Microbial Study, researchers identified two Aspergillus fumigatus strains isolated from the HEPA filter and the surface of the cupola of the ISS. Initial whole genome sequence analysis identified the isolates as A. fumigatus. This fungus can cause opportunistic infection termed aspergillosis in individuals with a compromised immune system. A long journey in space may actually compromise the immune system and make astronauts more susceptible to diseases. Researchers also conducted pathogenicity tests using the zebrafish larval model and determined that ISSF-21 is more virulent than two clinical strains (Af293 and CEA10); virulence for strain IF1SW-F4 is still being tested.
In this study, researchers present the draft genome sequences of the two strains, obtained through whole-genome sequencing.
Thousands of yeast strains from the Yeast Deletion Collection were flown on Space Shuttle flight STS-135 to the ISS in an experiment to identify genes required for survival in microgravity. Each individual strain was a mutant of the species Saccharomyces cerevisiae (brewer's yeast) that carried a deletion in a single gene. The deletion was marked by a "barcode" DNA sequence to allow identification of the surviving strains after flight. The strains were pooled together to allow competition for growth over approximately 21 generations during the spaceflight experiment. Strains missing from the mix after flight had deletions in genes that were required for survival.
This investigation was funded by the NASA Space Biology Program Office grant NNX10AP01G.
Primary cultures from mouse bone marrow were induced to differentiate by the presence of recombinant macrophage colony stimulating (rM-CSF) factor for 14-days during spaceflight. Cells were fixed to preserve RNA during flight and returned to Earth for transcriptional profiling using microarray analysis. Complementary analyses included cell proliferation studies and flow cytometry to detect antigens specific to the macrophage lineage.
This investigation was funded by the NASA Space Biology Program Office grant NNX08BA91G and also supported by the American Heart Association grant 0950036G, NIH grants AI55052, AI052206, AI088070, RR16475 and RR17686, the Jerry C. Johnson Center for Basic Cancer Research and the Kansas Agriculture Experiment Station.
During germination, a calcium current is triggered in the fern spore by a gravity sensing mechanism. The calcium current is part of a signalling cascade that orients the growth of the fern. Prior studies have determined that the critical timepoint for the gravity signal in the germination process occurs ten hours after the light signal that causes the onset of germination. In this study, transcriptional analysis was performed at ten hours post-germination to identify genes potentially important for the gravity response.
This study was supported by NASA Space Biology grants NNX09AH45G, NNX09AB41A, and NNX11AF48A to D. Marshall Porterfield and NSF grant IOS-1027514 to Stanley J. Roux
Liver is the metabolic hub of the vertebrate organ system and is involved in detoxification, regulation of glycogen storage, protein synthesis, and digestion, among other functions. Previous spaceflight experiments have demonstrated many changes in liver gene expression and in the activity of liver enzymes. GeneLab engaged in a sample sharing mission with the Rodent Research-1 (RR-1) project (GLDS-48) and with NASA's ISS National Lab managed by CASIS (GLDS-47) to provide tissue processing and extensive omics analyses on liver tissue from mice flown in microgravity. The RR-1 mission comprised the maiden voyage and validation of NASA's Rodent Research Hardware System. The RNA, protein, and DNA methylation data sets released here complement previous omics analyses from rodents in spaceflight and can be part of longitudinal studies for future rodent missions.
For the NASA investigation, samples were provided to GeneLab by the Rodent Research-1 project. The investigation was funded by the NASA Space Biology Program Office, Space Life and Physical Sciences Research and Applications Division, and additional funding from the International Space Station Research Integration Office to the Space Biology GeneLab Project.
For the National Lab investigation, samples were provided to GeneLab by Dr. Sam Cadena (Novartis Institutes for Biomedical Research) through the Rodent Research-1 project. This investigation was funded by the Center for Advancement of Science in Space (CASIS), the NASA Space Biology Program Office, Space Life and Physical Sciences Research and Applications Division and additional funding from the International Space Station Research Integration Office to the Space Biology GeneLab Project.
This study provides a ground to microgravity comparative gene expression data set of female C57BL/6J mice utilizing transcriptional microarray technology. This data release in conjunction with data from previous studies in spleen and thymus using mice flown on the same mission, will allow researchers to perform network analyses that will help to gain a better understanding of the precise mechanisms that result in changes and possible health consequences associated with spaceflight.
This study was supported by the NASA Cooperative Agreement NNX10AJ31G “Cooperative Research in Proton Space Radiation", the LLUMC (Loma Linda University Medical Center) Department of Radiation Medicine and the University of Colorado Anschutz Medical Center Department of Anesthesiology. Liver samples were obtained through the NASA Biospecimen Sharing Program.
Built environments like the ISS are known to have their own microbiomes. Next-generation sequencing methods are being used to explore the ISS microbial profile to enable the development of appropriate safety and maintenance practices. This study provides strong evidence that specific human skin-associated microorganisms constitute a significant population of the ISS microbiome, generating notable differences between the ISS microbiome and cleanrooms on Earth.
This research was funded by NASA Space Biology Grant no. 19-12829-27 under Task Order NNN13D111T award to K. Venkateswaran.
This study provides a ground-to-microgravity comparative gene expression analysis of Arabidopsis thaliana seedlings. The core project examines global gene expression by RNASeq and the composition of the soluble protein fraction. The GeneLab collaboration augments the core investigation with an additional membrane protein data set. The data will allow researchers to perform network analyses to add to the knowledge of physiological effects of spaceflight during seedling growth.
This competitively selected study was funded by the NASA Space Biology Program Office, Space Life and Physical Sciences Research and Applications Division, NASA Taskbook Grant NNX13AM48G to Sarah Wyatt and additional funding from the International Space Station Research Integration Office to the Space Biology GeneLab Project.
The core study characterizes transcriptional patterns of Arabidopsis thaliana induced during germination and growth on the International Space Station. The GeneLab collaboration allows the comparative study of three additional ecotypes. This investigation will aid researchers in assessing the common and ecotype-specific effects of spaceflight on gene expression and will facilitate cross-study data comparisons with future experiments utilizing these strains. This data release includes 48 out of 56 sample expression files with the remaining 8 files to be released at a later date.
This competitively selected study was funded by the NASA Space Biology Program Office, Space Life and Physical Sciences Research and Applications Division, NASA Taskbook Grant No. NNX13AM50G to Simon Gilroy and additional funding from the International Space Station Research Integration Office to the Space Biology GeneLab Project.
This study investigates the effects of microgravity during spaceflight on bone loss due in part to decreased bone formation by unknown mechanisms. Because it is difficult to perform experiments in space, researchers used ground-based simulators such as the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM) to study the microgravity environment. In this study, researchers exposed 2T3 preosteoblast cells to the RWV for 3 days and found that alkaline phosphatase activity, a marker of differentiation, was inhibited. In addition, they found 61 genes downregulated and 45 genes upregulated by more than twofold compared to static 1 g controls, as shown by microarray analysis. These mechanosensitive genes may provide novel insights into understanding the mechanisms regulating bone formation and potential targets for countermeasures against decreased bone formation during spaceflight and in pathologies associated with lack of bone formation.
Using an Earth-based microgravity simulation technique that utilizes a high gradient magnetic field to levitate a biological organism, researchers investigated the biological response to weightlessness in D. melanogaster. From these experiments, researchers observed a delay in the development of the fruit flies from embryo to adult. Microarray analysis indicated significant changes in the expression of immune-, stress-, and temperature-response genes.
This study investigates the effects of microgravity on Murine Bone Marrow Stromal Cells (BMSC) that were flown to the International Space Station. The researchers use Genechip technology to detect differences in cell proliferation and cell-cycle genes between flight and control samples. This study represents the first report on the behavior of the potentially osteogenic murine BMSC in a 3D culture system.
Spores of B. subtilis 168 were exposed to real space conditions and to simulated Martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Using microarray technology, this study reveals a change in expression of stress-related regulons responding to DNA damage.
Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.
Researchers investigated both transcriptomic and proteomic changes in R. rubrum S1H cultures after a 10-day flight on the International Space Station and compared results to corresponding ground controls. Ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. Whole-genome oligonucleotide microarray was used to test the effects of space flight. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which allows distinguishing the different factors acting in spaceflight conditions.