Data Release Announcements

April 28, 2017 —
Transient gene expression profile changes of confluent human fibroblast cells in spaceflight
human fibroblast cells
Confluent (non-dividing) culture of human fibroblast cells.
Credit: NASA/Honglu Wu

Microgravity, or an altered gravity environment from the static 1g, has been shown to influence global gene expression patterns and protein levels in cultured cells or animals. However, it is unclear how these changes in gene and protein expressions are related to each other or are related to other factors regulating such changes. Recent advancements in the field of molecular biology revealed that a different class of RNA, the small non-coding microRNA (miRNA), can have a broad effect on gene expression networks by mainly inhibiting the translational process. In this experiment conducted on the International Space Station, the hypotheses to be tested are: miRNA profiles will be altered in the space environment, and cellular responses to DNA damage in space are different from those on the ground.

This work was supported by the NASA Fundamental Space Biology Program.

April 28, 2017 —
STS-135 liver metabolomics
mice
Scientists have found that mice showed early signs of liver disease after only two weeks in space.
Credit: NASA

Mice were flown onboard STS-135 and returned to Earth for analysis. Livers were collected within 3-4 hours of landing and snap frozen in liquid nitrogen. Samples were shipped to Metabolon, Inc. for analysis.

This study was supported by the NASA Cooperative Agreement NNX10AJ31G 'Cooperative Research in Proton Space Radiation' and NNX10AE39G, the 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.

April 28, 2017 —
Biological and metabolic response in STS-135 space-flown mouse skin
astronaut in space
NASA astronaut Nicole Stott, Expedition 20/21 flight engineer, is pictured near the Mice Drawer System (MDS) in the Kibo laboratory of the ISS. Results from the MDS have shown premature aging in mouse skin after three months in microgravity.
Credit: NASA

To explore possible mechanisms, changes in gene expression profiles implicated in oxidative stress and in ECM remodeling in mouse skin were examined after space flight. The metabolic effects of space flight in skin tissues were also characterized.

This study was supported by NASA grant NNX10AJ31G and the LLUMC Dept. of Radiation Medicine.

April 28, 2017 —
Effect of microgravity on an animal-bacteria symbiosis
squid
Studying the impact of microgravity on the interactions between the squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri.
Credit: Jamie S. Foster, Ph.D., University of Florida

Spaceflight imposes numerous adaptive challenges for terrestrial life. The reduction in gravity or microgravity, represents a novel environment that can disrupt homeostasis of many physiological processes. Additionally, it is becoming increasingly clear that an organism’s microbiome is critical for host health and examining its resiliency in microgravity represents a new frontier for space biology research. In this study, we examine the impact of microgravity on the interactions between the squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri, which form a highly specific binary mutualism. First, animals inoculated with V. fischeri aboard the space shuttle showed effective colonization of the host light organ, the site of the symbiosis, during space flight. Second, RNA-Seq analysis of squid exposed to modeled microgravity conditions exhibited extensive differential gene expression in the presence and absence of the symbiotic partner. Transcriptomic analyses revealed in the absence of the symbiont during modeled microgravity there was an enrichment of genes and pathways associated with the innate immune and oxidative stress response. The results suggest that V. fischeri may help modulate the host stress responses under modeled microgravity. This study provides a window into the adaptive responses that the host animal and its symbiont use during modeled microgravity.

This study was supported by NASA Space Biology program grant NNX13AM44G.

  • Principal Investigator: Jamie Foster
  • Organism: Euprymna scolopes
  • Data Type: Transcription profiling by high-throughput sequencing
  • Study Link: genelab-data.ndc.nasa.gov
April 28, 2017 —
Proteomics and transcriptomics analysis of Arabidopsis seedlings in microgravity New datasets added to GLDS-38: Hardware control RNAseq and proteomics data
seedlings
A comparison of Arabidopsis seedlings grown on Earth and in microgravity.
Credit: NASA

The samples were generated from protein and RNA extracts of Arabidopsis seedlings grown in mock BRIC hardware and were grown simultaneously with the ground control samples from the BRIC-20 study. “n2” samples were preserved by direct submersion in liquid nitrogen, whereas the “rl” samples were submerged in RNAlater for 12 hours prior to freezing at -80C. The protein and RNA extracts were analyzed in the same manner as the space flight and ground control samples.

  • Principal Investigator: Sarah Wyatt
  • Organism: Arabidopsis thailana
  • Data Type: Transcription profiling by high-throughput sequencing and protein expression profiling by mass spectrometry
  • Study Link: genelab-data.ndc.nasa.gov
April 28, 2017 —
Expression Data from International C. elegans Experiment 1st (ICE-FIRST)
C. elegans
The roundworm C. elegans
Credit: NASA

The effect of microgravity on gene expression in C.elegans was comprehensively analyzed by DNA microarray (Agilent). Hypergravity and clinorotation experiments were performed as reference against the flight experiment. Mix staged C. elegans N2 was exposed microgravity for 10 days.

ICE-FIRST was a collaborative effort among four nations: France, United States, Japan, and Canada.

  • Principal Investigator: Akira Higashibata
  • Organism: Caenorhabditis elegans
  • Data Type: Transcription profiling by array
  • Study Link: genelab-data.ndc.nasa.gov
April 28, 2017 —
The Role of PTHrP in Osteoblast Response to Microgravity: Implications for Osteoporosis Development
astronaut
Astronaut exercising on the ISS.
Credits: JAXA/NASA

Prolonged skeletal unloading through bedrest results in bone loss similar to that observed in elderly osteoporotic patients, but with an accelerated timeframe. This rapid effect on weight-bearing bones is also observed in astronauts who lose up to 2% of their bone mass per month spent in space. Despite important implications for space-flight travelers and bedridden patients on Earth, the exact mechanisms involved in disuse osteoporosis have not been elucidated. Parathyroid hormone-related protein (PTHrP) regulates many physiological processes including skeletal development, and has been proposed as a gravisensor. To investigate the role of PTHrP in microgravity-induced bone loss, trabecular osteoblasts (TOs) from Pthrp+/+ and -/- mice were exposed to simulated microgravity for 6 days. Viability of TOs decreased in inverse proportion to PTHrP expression levels. Microarray analysis of Pthrp+/+ TOs after 6 days at 0g revealed expression changes in genes encoding prolactins, apoptosis and survival molecules, bone metabolism and extra-cellular matrix composition proteins, chemokines, IGF family and Wnt-related signaling molecules. Importantly, 88% of 0g-induced expression changes in Pthrp+/+ cells overlap those observed in Pthrp-/- cells in normal gravity. Pulsatile treatment with PTHrP1-36 peptide during microgravity exposure reversed a large proportion of 0g-induced changes in Pthrp+/+ TOs. Results confirm PTHrP efficacy as an anabolic agent to prevent microgravity-induced cell death in TOs. Total RNA samples extracted from Pthrp+/+and -/- trabecular osteoblasts (TOs) exposed for 6 days to simulated 0g in Synthecon rotating cell, or left 6 days in culture at 1g. Cells had either been treated with a pulsatile treatment (2 h/day) of PTHrP1-36 peptide (10-8M) or received a change in growth medium.

This work was completed through the Canadian Space Agency (CSA) E/Osteo program contract # 9F-007-05-1657 and a grant to Dr. David Goltzman from the Canadian Institutes of Health Research (FRN-86703).

April 28, 2017 —
Microgravity effect on C. elegans N2/VC (CERISE, 4 days)
C. elegans
Magnified image of C. elegans, two adult worms and one juvenile worm, crawling in liquid media.
Credit: NASA

The effect of microgravity on C. elegans gene expression was analyzed by the whole genome microarray. The worms were cultivated under microgravity for 4 days in the Japanese module of the International Space Station. C. elegans N2 were exposed to microgravity for 4 days. The worms synchronously were cultivated from L1 larvae to adult. There were two control groups, onboard 1G and ground 1G control.

This experiment was supported by the Cell Biology Experiment Project conducted by the Institute of Space and Astronautical Science in JAXA, and was funded in part by JSPS KAKENHI Grant Numbers 26506029, 15H05937, the Medical Research Council UK (G0801271), and National Institutes of Health (NIH NIAMS ARO54342).

April 28, 2017 —
The influence of simulated microgravity on the proteome of Daphnia magna
water flea
The water flea Daphnia
Credit: Nature World News

The water flea Daphnia is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space. In this study, a proteomic approach was used to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity generated by a 2D-clinostat. Five biological replicates were analyzed using 2D-DIGE proteomic analysis. Identified were 109 protein spots differing in intensity (p < 0.05). Substantial fractions of these proteins are involved in actin microfilament organization, indicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity induced break-down of protein structures in general. In addition, simulated microgravity increased the abundance of energy metabolism related proteins, indicating an enhanced energy demand of Daphnia. Most of the Daphnia protein sequences are well conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept.

Financial support was received from BMWi and DLR (Grant No. 50WB1029), as well as the ESA-GBF-program (Contract No. 4000103571).

April 28, 2017 —
Global gene expression analysis highlights microgravity-sensitive key genes in soleus and EDL of 30 days space flown mice
mouse with detailed diagram of leg muscles
Credit: NeuroDojo

Microgravity exposure as well as chronic muscle disuse are two of the main causes of physiological adaptive skeletal muscle atrophy in humans and murine animals. The aim of this study was to investigate, at both morphological and global gene expression levels, skeletal muscle adaptation to microgravity in mouse soleus and extensor digitorum longus (EDL). Adult male mice C57BL/N6 were flown aboard the BION-M1 biosatellite for 30 days on orbit (BF) or housed in a replicate flight habitat on Earth (BG) as reference flight control. This study investigated for the first-time, gene expression adaptation to 30 days of microgravity exposure in mouse soleus and EDL, highlighting potential new targets for improvement of countermeasures able to ameliorate or even prevent microgravity-induced atrophy in future spaceflights. C57BL/N6 mice were randomly divided in 3 groups: Bion Flown (BF), mice flown aboard the Bion M1 biosatellite in microgravity environment for 30 days; Bion Ground (BG), mice housed in the same habitat of flown animals but exposed to earth gravity; and Flight Control (FC), mice housed in a standard animal facility.

This work was supported from grants of the Department of Economics and Technology of the German Government (BMWi) through the German AeroSpace Board, Deutsches Zentrum fur Luftund Raumfahrt (DLR), e.V. Bonn, Germany (grant # 50WB821 and 1121 to DB).

April 28, 2017 —
Gene expression profile changes due to bleomycin-induced DNA damage in human fibroblasts in space
human fibroblast cell
Human fibroblast cell
Credit: Jiashan Wang

The purpose of this study was to understand gene expression responses in confluent human fibroblasts in microgravity conditions to bleomycin treatment. Confluent human fibroblasts AG01522 were flown to the International Space Station (ISS). After three day on ISS, the cells were treated with bleomycin at 1.0 μg/mL for 3 hours. The cells were washed and fixed with RNALater. Total RNA were isolated after the samples were returned to Earth and subjected to microarray analysis.

This work was supported by the NASA Fundamental Space Biology Program.

April 28, 2017 —
Streptococcus mutans differential gene expression in response to simulated microgravity
Streptococcus mutans
Streptococcus mutans, bacteria found in the mouth, contributes to tooth decay.
Credit: Encyclopedia Britannica

Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, High Aspect Ratio Vessel (HARV) S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H2O2 resistance, and competence in sucrose-containing biofilm media.

Stationary phase S. mutans simulated microgravity cultures displayed increased killing by H2O2 compared to normal gravity control cultures, but competence was not affected. RNA-seq analysis revealed that expression of 153 genes was up-regulated 2-fold and 94 genes down-regulated 2-fold during simulated microgravity HARV growth. These included a number of genes located on extrachromosomal elements, as well as genes involved in carbohydrate metabolism, translation, and stress responses. Collectively, these results suggest that growth under microgravity analog conditions promotes changes in S. mutans gene expression and physiology that may translate to an altered cariogenic potential of this organism during space flight missions. Differential gene expression was compared between RNA from S. mutans grown in normal gravity HARVs (n=3 independent cultures) and RNA from S. mutans grown in simulated microgravity HARVs (n=3 independent cultures).

This work was funded by 2012 NASA Space Biology solicitation NNH12ZTT001N.

  • Principal Investigator: Kelly Rice
  • Organism: Streptococcus mutans
  • Data Type: Transcription profiling by high throughput sequencing
  • Study Link: genelab-data.ndc.nasa.gov
April 28, 2017 —
Gene expression profiling in human fibroblast after low-LET irradiation
fibroblast cells
Human fibroblast
Credit: EZ Biosystems

Exposure to radiation provokes cellular responses controlled in part by gene expression networks. MicroRNAs (miRNAs) are small non-coding RNAs which mostly regulate gene expression by degrading the messages or inhibiting translation. Here, we investigated changes in miRNA expression patterns after low (0.1 Gy) and high (2.0 Gy) doses of X-ray in human fibroblasts. At early (0.5 h) and late (6 and 24 h) time points, irradiation caused qualitative and quantitative differences in the down-regulation of miRNA levels, including miR-92b, 137, 660, and 656. A transient up-regulation of miRNAs was observed after 2 h post-irradiation following high doses of radiation, including miR-558 and 662. MicroRNA levels were inversely correlated with targets from mRNA and proteomic profiling after 2.0 Gy of radiation. MicroRNAs miR-579, 608, 548-3p, and 585 are noted for targeting genes involved in radioresponsive mechanisms, such as cell cycle checkpoint and apoptosis. We suggest here a model in which miRNAs may act as hub regulators of specific cellular responses, immediately down-regulated so as to stimulate DNA repair mechanisms, followed by up-regulation involved in suppressing apoptosis for cell survival. Taken together, miRNAs may mediate signaling pathways in sequential fashion in response to radiation, and may serve as biodosimetric markers of radiation exposure. The gene expression patterns in human fibroblasts after 2.0 Gy of low-LET radiation was determined at 2 and 24 hrs post-irradiation time in technical triplicates. Control non-irradiated samples were also prepared in triplicates.

This work was funded by National Aeronautics and Space Administration, NASA Johnson Space Center, Houston, Texas. Grant Number: NNJ06HF62G.

  • Principal Investigator: Eugenia Wang
  • Organism: Homo sapiens
  • Data Type: Transcription profiling by array
  • Study Link: genelab-data.ndc.nasa.gov
April 28, 2017 —
Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure - Identification of Regulatory Gene Network
human heart
Human heart
Credit: Dreamstime

We examined molecular responses using transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) iron (56Fe) particles, 1, 3, 7, 14 and 28 days after exposure. Unsupervised clustering analysis of gene expression segregated samples according to the radiation (IR) response, and time after exposure with 56Fe-IR showing the greatest level of gene modulation. 1H-IR exposures showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Individual transcription factors were inferred to be active at 1, 3, 7, 14 and 28 days after exposure. Validation of the signal transduction network by protein analysis showed that particle IR clearly regulates a long-lived signaling mechanism for p38 MAPK signaling and NFATc4 activation. Electrophoresis mobility shift assays supported the role of additional key transcription factors GATA-4, STAT-3 and NF-kB as regulators of the response at specific time points. These data suggest that the molecular response to 56Fe-IR is unique and shows long-lasting gene expression in cardiomyocytes, up to 28 days after exposure. Additionally, proteins involved in signal transduction and transcriptional activation via DNA binding play a role in the response to high charge (Z) and energy (E) particles (HZE). Our study may have implications for NASA's efforts to develop heart disease risk estimates for astronauts’ safety via identification of specific HZE-IR molecular markers and for patients receiving conventional and particle radiotherapy.

This work was supported by NASA and American Heart Association to D. A. Goukassian. This work was also supported in part by the U.S. Department of Energy (DOE) with funding from the U.S. DOE Low Dose Radiation Research Program to M. A. Coleman. The AHA and National Heart, Lung, and Blood Institute supported X. Yan. This work was also supported by National Space Biomedical Research Institute (NSBRI) to M. Natarajan.

March 24, 2017 —
Multi-omic data from nine mouse organs from Rodent Research-1 mission New 5-methyl-cytidine analysis enables examination of post-transcriptional epigenetic RNA regulation
mice
NASA's Rodent Research mission includes experiments to develop countermeasures for bone and muscle loss.

NASA's Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. In the current set of investigations, GeneLab performed epigenomic, transcriptomic, and proteomic assays on DNA, RNA, and protein extracted from archived RR–1 tissue samples. At the end of the RR–1 mission, mice samples were collected. A variety of tissue types were harvested and either snap-frozen or preserved with RNAlater, and then stored at least a year at -80°C. Tissues available for analyses were prioritized based on the likelihood of significant scientific value in the context of either astronaut effects or previously documented rodent tissue effects. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands, quadriceps, gastrocnemius, tibialis anterior, extensor digitorum longus, soleus, eye, kidney and liver. In addition to providing other opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues, our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities.

GeneLab is proud to announce that we have included 5–methyl–cytidine (m5C)–RNAseq analysis for some of the RR–1 tissues including liver, kidney, quadriceps, gastrocnemius, and tibialis anterior. m5C residues are present in both coding and non-coding RNAs as well a the more commonly known reversible epigenetic marking of DNA on 5–methyl cytosine known to regulate transcription.

This investigation was funded by the NASA Space Biology Program Office, Space Life and Physical Sciences Research and Applications Division with additional funding from the International Space Station Research Integration Office to the Space Biology GeneLab Project.

March 24, 2017 —
Bacterial gene expression profiling in microgravity Gene expression profiling suggests increased toxicity in medium of cultured bacteria confirming reduced extracellular mass transport in microgravity
astronaut working aboard the ISS
Astronaut Rick Mastracchio works on the Antibiotic Effectiveness in Space-1 (AES–1) investigation during Expedition 38 aboard the International Space Station. AES–1 consists of a Commercial Generic Bioprocessing Apparatus (CGBA) and 16 Group Activation Packs (GAPs).

Bacterial behavior has been observed to change during spaceflight. Higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics have been reported to occur for cells cultured in space. Most of these phenomena are theorized as being an indirect effect of an altered extracellular environment, where the carbon source uptake is inhibited and excreted acidic byproducts buildup around the cell due to the lack of gravity-driven transport forces. The gene expression results from this spaceflight mission entitled Antibiotic Effectiveness in Space–1 (AES–1) corroborate this hypothesis: the data indicate an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity - all of which can be associated with reduced extracellular mass transport.

The data analysis effort for this investigation was funded under Grant Agreement (GA-2014-146) as part of the International Space Station (ISS) National Laboratory through the Center for the Advancement of Science in Space, Inc. (CASIS) in accordance with NASA Cooperative Agreement No. NNH11CD70A (http://www.iss-casis.org/). Luis Zea's work in Germany was funded by the German Academic Exchange Service (DAAD) and the German Aerospace Center (DLR) for their support through the DAAD Research Fellowship for Doctoral Candidates and Young Scientists (https://www.daad.org/).

  • Study Title: A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space
  • Principal Investigator: David M. Klaus, Ph.D., BioServe Space Technologies, Boulder, CO, United States
  • PI Website: http://www.colorado.edu/aerospace/david-klaus
  • Organism: Escherichia coli
  • Data Type: transcription profiling by high throughput sequencing
  • Study Link: genelab-data.ndc.nasa.gov
March 24, 2017 —
DNA copy number analysis from mice with cosmic radiation-induced acute myeloid leukemia GeneLab highlights gene deletion in mice irradiated by 1 GeV/nucleon 56Fe ions
figure A figure B
Both high- and low–LET radiation-induced rAML show hemizygous deletion of chromosome 2 including the PU.1 gene. (A) Deletion of chromosome 2 in rAML spleen cells was assessed by FISH with a PU.1–containing BAC probe (pink) and DNA was counterstained with DAPI (blue). Cells were scored as having a hemizygous deletion if signals were absent from both chromatids of one chromosome 2 homolog. Representative metaphases are shown with 10 um scale bars. (B) Array CGH was used to identify deletions on chromosome 2. The location of PU.1 is indicated with a vertical line. Chromosomal gains (blue) and losses (red) are depicted for individual AML samples, demonstrating single copy PU.1 loss in all cases except AML 2704. Adapted from Mutagenesis. 2013 Jan; 28(1): 71–79.

Certain mouse strains such as CBA, C3H and RFM, have high incidence of radiation-induced acute myeloid leukemia (AML). The data in this series was generated by using spleen DNA from Male CBA/CaJ mice irradiated at 8–14 weeks of age with either gamma-rays or heavy ion (1 GeV/nucleon 56Fe ions) particles. Spleen DNA with radiation-induced AML was compared with DNA from normal CBA mice. Array comparative genomic hybridization were used to show that PU.1 mutations are common in both low-LET and high-LET rAML. The manuscript describing the full data highlights the similarities in molecular characteristics of high-LET and low-LET rAML and confirm the presence of ongoing chromosomal and microsatellite instability in murine rAML.

This study was funded by an NSCOR grant from the National Aeronautics and Space Administration (NAG-1569 to M. Weil); the US Department of Energy Low Dose Radiation Research Program (DE-FG02-05ER63946 to M. Weil and R. Ulrich); and the National Aeronautics and Space Administration (NNX07AP85G to J. Bedford and Y. Peng)

March 24, 2017 —
GeneLab highlights gene expression in multi-generation study on fruit fly grown both in space and earth over multiple generations Gene expression of multi-generation study on Drosophila melanogaster
figures a, b, c
Distribution of differentially expressed genes among pairwise comparisons of the study groups. (A) DEG distribution according to the biological processes. (B) DEG distribution according to the cellular compartments. (C) DEG distribution according to the molecular functions. Figure from PLoS One. 2016; 11(11): e0166885.

In prospective human exploration of outer space, the need to maintain a species over several generations under changed gravity conditions may arise. This paper reports the analysis of the third generation of fruit fly Drosophila melanogaster obtained during the 44.5-day space flight (Foton–M4 satellite, 2014, Russia), followed by the fourth generation on Earth and the fifth generation under conditions of a 12-day space flight (2014, in the Russian Segment of the ISS).

The study was supported by the program of fundamental research SSC RF–IBMP RAS, program Cell and Molecular Biology of the RAS Presidium.

  • Study Title: The development of Drosophila melanogaster during space flight
  • Principal Investigator: Irina Ogneva, State Scientific Center of Russian Federation Institute of Biomedical Problems of the Russian Academy of Sciences
  • Organism: Drosophila melanogaster
  • Data Type: transcription profiling by high throughput sequencing
  • Study Link: genelab-data.ndc.nasa.gov
March 24, 2017 —
Gene-expression profiling of Saccharomyces cerevisiae irradiated by high- and low- LET radiations Oxidative stress is confirmed to be the key response in yeast cells exposed to most types of ionizing radiation
yeast
Saccharomyces cerevisiae - Wikipedia

Ionizing radiations are categorized by linear energy transfer (LET). High–LET are primarily found in space and have been shown to have a higher relative biological effectiveness (RBE) than low–LET radiations for many processes. This data–set provides gene-expression in yeast exposed to high–LET radiations (fast neutron, heavy ion (C) and thermal neutron) and low–LET radiation (gamma ray). Oxidative stress response is seen for all four types of radiation, but high–LET radiations induce a stronger response in these pathways. Such data are critical to evaluate the unique response of living cells exposed to a radiation environment only found in space and evaluate its RBE.

This study was supported in part by the Budget for Nuclear Research of the Ministry of Education, Culture, Sports, Science and Technology, based on screening and counseling by the Atomic Energy Commission. This work was carried out in part under the Visiting Researcher's Program of the Research Reactor Institute of Kyoto University and Research Project with Heavy Ions at NIRS-HIMAC

  • Study Title: Gene-expression profiling of Saccharomyces cerevisiae irradiated by high-LET radiations
  • Principal Investigator: Hitoshi Iwahashi, Ph.D., Japanese National Institute of Advanced Industrial Science and Technology
  • PI Website: http://www.abios.gifu-u.ac.jp/h1884/
  • Organism: Saccharomyces cerevisiae
  • Data Type: transcription profiling by array
  • Study Link: genelab-data.ndc.nasa.gov
March 24, 2017 —
Global gene expression responses to low doses of protons in a human 3-dimensional skin model Novel gene pathways for dose response of human skin mimetic tissue to low-LET protons
skin mimetic 3D model
EPI-200 skin mimetic 3D model (adapted from mattek.com)

Accumulating data suggest that the biological responses to high and low doses of radiation are qualitatively different, necessitating the direct study of low dose responses. Most such studies have utilized 2–dimensional culture systems, which may not fully represent responses in 3–dimensional tissues. This data-set provides changes in gene expression in EPI-200, a 3–dimensional tissue model that imitates the structure and function of human epidermis, at 4, 16 and 24 hours after exposure to high (2.5 Gy) and low (0.1 Gy) doses of low LET protons. Highlight of the published analysis on these data showed that low dose was associated with gradual recovery and tissue remodeling, with HNF4A being a novel transcription factor not previously associated with radiation response, being most prominent in the low dose response.

This work was supported by the Office of Science (BER), U.S. DOE, Grant No. DE-FG02-07ER46336, and by grant number P41 EB002033-13, Radiological Research Accelerator Facility (RARAF), from the National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIBIB).

March 24, 2017 —
Heavy ion particle radiation has different responses in both humans and mice Responses in different mice strains may hold key to genes involved in radiation damage risk
DNA
An artist's concept of DNA battered by heavy ions from space; heavy ions are more damaging than X–rays. Credit: NASA/OBPR.

Carbon–ion (C–ion) radiation is used to treat tumors and humans are heterogeneous in their response to the treatment. Astronauts are exposed to whole body, chronic cosmic radiation, where protons and heavy ions are an important component and genetic differences in humans may allow some astronauts to withstand radiation better than others. There are hundreds of inbred strains of mice and strain differences have been important to the elucidation of disease mechanisms since different strains respond differently to diseases - including those caused by radiation damage. In this study, the authors performed whole lung C–ion irradiation using three different strains of mice to examine whether strain-dependent differences in radiation effects occur in high–LET C–ion thoracic irradiation. Microarray analysis was used to identify the key genes that are differentially regulated in different mouse strains after C–ion irradiation and to determine the mechanism of strain-dependent pulmonary damage after high–LET C–ion irradiation. The authors identified candidate molecules that could be implicated in the between-strain variance to early hemorrhagic pneumonitis after C–ion irradiation.

This research was supported in part by the funds for Research Project with Heavy Ions at National Institute of Radiological Sciences-Heavy Ion Medical Accelerator in Chiba (NIRS-HIMAC), Japan.

October 26, 2016 —
Sequencing of mouse, E. coli and bacteriophage DNA in space using Oxford Nanopore MinION DNA sequencing in space could revolutionize research and environmental monitoring
Biomolecule Sequencer
Astronaut Kate Rubins and the first DNA sequencing data obtained in space. The grey rectangular object below the computer screen is the MinION sequencer.

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.

September 21, 2016 —
Microbial monitoring of the Kibo Japanese Experiment Module of the International Space Station Heavily used surfaces were monitored during three missions from 2009 to 2012

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.

September 21, 2016 —
Response of B. subtilis to low pressure may give clues to potential for bacterial survival in extreme environments like Mars Earth-based study uses hypobaric chambers to mimic low-pressure environments

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)

September 21, 2016 —
Response of human lung cells in culture to heavy particle radiation Study may aid in assessing lung cancer risk for astronaut safety

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

  • Study Title: Transcriptome Profiles in Normal Human Bronchial Epithelial Cells after Exposure to gamma-rays and different HZE particles
  • Principal Investigator: Michael Story, Ph.D.; University of Texas Southwestern Medical Center
  • PI Website: http://www.utsouthwestern.edu/labs/story/
  • Organism: Human bronchial epithelial cell line HEBC3KT
  • Data Type: Transcription profiling by microarray
  • Study Link: genelab-data.ndc.nasa.gov
September 21, 2016 —
Study models breast cancer risk due to Galactic Cosmic Radiation exposure Mouse breast tumor model used to characterize gene expression after exposure

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)

September 21, 2016 —
Mechanism of breast cancer induction post-irradiation modeled in mouse Children exposed to ionizing radiation have increased risk of breast cancer

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

September 21, 2016 —
Ionizing radiation alters tumor microenvironment to enhance tumor growth Mouse tumors implanted into irradiated hosts have differing tumor potentials depending on type of radiation exposure of the host tissue

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.

September 21, 2016 —
Human mammary epithelial cells exposed to ionizing radiation and the cytokine TGFbeta Combined effect causes cells to develop signatures of cancer cells

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).

  • Study Title: Transcription profiling of human MCF10A cells subjected to ionizing radiation and treatment with transforming growth factor beta-1
  • Principal Investigator: Mary Helen Barcellos-Hoff, PhD; University of California San Francisco
  • PI Website: http://cancer.ucsf.edu/people/profiles/barcellos-hoff_mary.6915
  • Organism: Homo sapiens (human mammary epithelial cells)
  • Data Type: Transcription profiling by microarray
  • Study Link: genelab-data.ndc.nasa.gov
September 21, 2016 —
Effect of simulated microgravity on global transcription studied in Zebrafish larvae Two-dimensional clinorotation during early development used to mimic microgravity

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

September 21, 2016 —
Space effects studied in Japanese Medaka fish Fish lived on board the ISS for two months during 2012

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)

September 21, 2016 —
Worm experiment highlights potential therapeutic pathway to combat spaceflight effects RNA interference to block muscle protein degradation works in space as well as on Earth

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.

September 21, 2016 —
The intestinal microbiome response to radiation and spaceflight studied in rodents Three experiments investigated effects of spaceflight, weightbearing, diet and radiation

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.

  • Study Title: Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis
  • Principal Investigator: Nancy Turner, Ph.D.; Texas A&M University
  • PI Website: http://nfs.tamu.edu/people/turner-nancy/
  • Organism: Intestinal microbiota from Mus musculus and Rattus norvegicus
  • Data Type: Metagenomic 16S rDNA pyrosequencing
  • Study Link: genelab-data.ndc.nasa.gov
September 21, 2016 —
Study helps pave the way toward future radiation biodosimetry sensor for astronauts Study mimics astronaut exposure to ionizing radiation to identify biomarkers of exposure

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.

September 21, 2016 —
Ground based study examines how suboptimal culture conditions affect transcriptional responses to altered gravity in Drosophila Responses to altered gravity are strongly affected by exposure to suboptimal temperature

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]

  • Study Title: Environmental and facility conditions promote singular gravity responses of transcriptome during Drosophila metamorphosis
  • Principal Investigator: Raul Herranz, Ph.D.; Spanish National Research Council, Madrid, Spain
  • Organism: Drosophila melanogaster
  • Data Type: Transcription profiling by microarray
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
GeneLab releases six datasets from International Space Station Microbial Observatory study ISS environmental sampling targets areas most used by crew members
petri dish with colonies of microbes
Petri dish containing colonies of microbes grown from a sample collected aboard the International Space Station.
Credits: NASA / JPL

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.

These investigations were funded by the NASA Space Biology Program Office grants 19-12829-26 and 19-12829-27 under Task order NNN13D111T.

July 10, 2016 —
Study designed to identify the microbial diversity of the International Space Station

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.

  • Study Title: Microbial Observatory (ISS-MO): Microbial diversity
  • Organism: Environmental Samples
  • Data Type: Metagenomic DNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
Metagenomics study targets functional genomic diversity of ISS microbiome

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.

  • Study Title: Microbial Observatory (ISS-MO): Indoor microbiome study of the International Space Station surfaces
  • Organism: Environmental Samples
  • Data Type: Metagenomic DNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
First study to show the reservoir of antimicrobial genes on the ISS

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.

  • Study Title: Microbial Observatory (ISS-MO): Antimicrobial Resistance Genes
  • Organism: Environmental Samples
  • Data Type: DNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
Study targets pathogenicity of International Space Station microbes

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..

  • Study Title: Microbial Observatory (ISS-MO): Study of BSL-2 bacterial isolates from the International Space Station
  • Organism: Environmental samples
  • Data Type: Whole genome DNA sequence data
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
Previously uncharacterized Bacillus species identified from samples taken on the ISS

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.

  • Study Title: Microbial Observatory (ISS-MO): Molecular characterization of Bacillus issensis, sp. nov., isolated from various quarters of the International Space Station
  • Organism: Bacillus from Environmental Samples
  • Data Type: Whole genome DNA sequence data
  • Study Link: genelab-data.ndc.nasa.gov
July 10, 2016 —
ISS Microbial Observatory: Aspergillus fumigatus strains isolated from the International Space Station

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.

  • Study Title: Microbial Observatory (ISS-MO): Draft Genome Sequence of two Aspergillus fumigatus Strains Isolated from the International Space Station
  • Organism: Aspergillus fumigatus from Environmental Samples
  • Data Type: Whole genome DNA sequence data
  • Study Link: genelab-data.ndc.nasa.gov
June 21, 2016 —
Genes Required for Survival in Microgravity Studied Using Yeast Investigator uses barcode tag to identify surviving yeast strains
yeast spores with barcode image overlay
The common brewer's yeast (Saccharomyces cerevisiae) was used to study the genes required for survival in the spaceflight environment. Thousands of mutant strains were co-cultured to determine which strains could out-compete the others. The winners were identified by virtue of a DNA "barcode" or genetic tag.

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.

June 21, 2016 —
Collaborative study of plant growth in space conducted by Japanese, Russian and American scientists and astronauts
  • Study Title: RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
  • Principal Investigator: Prof. Dr. Manabu Sugimoto, Okayama University, Japan
  • Organism: Brassica rapa var. nipposinica
  • Data Type: Transcription profiling using RNAseq
  • Study Link: genelab-data.ndc.nasa.gov
June 21, 2016 —
Variable gravity exposure in Zebrafish during early development
  • Study Title: Exposure of zebrafish larvae to relative microgravity between 5-6 days post-fertilization
  • Principal Investigator: Rasoul Nourizadeh, Ph.D.; Norwegian School of Veterinary Science, Oslo, Norway
  • Organism: Danio rerio
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
June 21, 2016 —
European experiment examines effects of long duration spaceflight on mouse skin
  • Study Title: Effect of a 91-day long stay in weightlessness on the International Space Station on mouse skin physiology
  • Principal Investigator: Betty Nusgens, Ph.D.; University of Liege, Belgium
  • Organism: Mus musculus
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
June 21, 2016 —
Microarray study examines transcriptional responses of yeast grown in microgravity - focus on cell-cell interactions required for mating, biofilm formation, and flocculation
  • Study Title: Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival
  • Principal Investigator: Katty V.Y. Goosens, Ph.D., Free University of Brussels, Belgium
  • Organism: Saccharomyces cerevisiae
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
June 21, 2016 —
Rodent transcriptome study spans the gravity continuum
  • Study Title: Transcription profiling of rat response to changes in developmental stage- 3 types of tissue, 3 gravity conditions, 2 developmental conditions
  • Principal Investigator: Karen Plaut, Ph.D.; Purdue University, West Lafayette, IN
  • Organism: Mus musculus
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Space Shuttle Mission STS-126 Mouse Macrophage Transcription Profiling Study Researchers profile transcriptional changes during differentiation of mouse primary bone marrow cells in microgravity
image of bioserve fpa
The Bioserve Fluid Processing Apparatus (FPA) was used to culture bone marrow cells on STS-126

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.

  • Study Title: Evaluation of in vitro macrophage differentiation during space flight
  • Principal Investigator: Stephen Chapes, Ph.D; Kansas State University
  • Organism: Mus musculus
  • Data Type: Transcription Profiling using Microarray
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Germinating Fern Spores Help Identify Genes Involved in Sensing and Responding to Gravity Study looks at RNA at critical time point in gravity sensing response
image of spore
A spore from the fern Ceratopteris richardii

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

  • Study Title: RNA-Seq analysis identifies potential modulators of gravity response in Ceratopteris spores: Evidence for modulation by calcium pumps and apyrase activity
  • Principal Investigator: Stanley J. Roux, Ph.D.; University of Texas at Austin
  • Organism: Ceratopteris richardii
  • Data Type: RNA-seq reference transcriptome, Ceratoperis, data released by GeneLab
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Additional Data from BRIC-19 Study on Arabidopsis Transcriptome Data from this study were originally released on November 1, 2015 under GeneLab accession number GLDS-37. An additional dataset is now available for this study.
  • Study Title: Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes
  • Principal Investigator: Simon Gilroy, Ph.D., University of Wisconsin, Madison
  • Organism: Arabidopsis thaliana
  • Data Type: Transcription Profiling using RNAseq
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Microarray Analysis of Muscle on the Effect of Countermeasures During Bedrest
  • Study Title: Woman skeletal muscle transcriptome with bed rest and countermeasures
  • Principal Investigator: Angele Chopard, Ph.D. Université de Montpellier, Montpelier, France
  • Organism: Homo sapiens
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
European Space Agency Experiment Profiles Transcription of Human Endothelial Cells in Microgravity
  • Study Title: Expression data from SPHINX (SPaceflight of Huvec: an INtegrated eXperiment)
  • Principal Investigator: Silvia Bradamante, Ph.D., Institute of Molecular Science and Technologies, Milan, Italy
  • Organism: Homo sapiens
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Microarray Study Compares Gene Expression in Astronaut Blood Samples Before and After Shuttle Missions
  • Study Title: Spaceflight Modulates Gene Expression in Astronauts
  • Principal Investigator: Jennifer Barrila, Ph.D., Arizona State University
  • PI Website Links: biodesign.asu.edu
  • Organism: Homo sapiens
  • Data Type: Transcription profiling using microarray
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
STS-135 Study Models Immune Response to Spaceflight Using Human Endothelial Cells
  • Study Title: Immune responses to the in vitro LPS assault engineered in the spaceflight multi-omics study
  • Principal Investigator: Meskerem Jibitu, US Army Center for Environmental Health Research, Fort Detrick, MD
  • Organism: Homo sapiens
  • Data Type: Multi-omic analysis
  • Study Link: genelab-data.ndc.nasa.gov
March 21, 2016 —
Ground Study Examines Changes in RNA in Human PBLs Cultured in Rotating Wall Vessels
  • Study Title: microRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity
  • Study Title: (additional): Gene expression profiling of human peripheral blood lymphocytes cultured in modeled microgravity
  • Principal Investigator: Maddalena Mognato, Ph.D., University of Padova, Italy
  • Organism: Homo sapiens
  • Data Type: Transcription profiling by Microarray
  • Study Link: genelab-data.ndc.nasa.gov
  • Study Link: (additional): genelab-data.ndc.nasa.gov
December 16, 2015 —
First Release of Epigenomic Data by GeneLab Omics analyses of mouse liver in microgravity on the Rodent Research-1 payload
liver section
The Habitat module of the Rodent Research Hardware System, shown with both access doors open.

Credits: NASA / Dominic Hart

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.

  • Study Title: Transcriptomics, Epigenomics and Proteomics of Mouse Liver from the Rodent Research-1 Spaceflight Payload
  • Principal Investigator: Ruth Globus (RR-1 Project Scientist), CASIS National Lab, GeneLab
  • PI Website Links: lsda.jsc.nasa.gov, nasa.gov
  • Organism: Mus musculus
  • Data Type: RNASeq, Whole Genome Bisulfite Sequencing, Proteomics
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Space Shuttle Mission STS-135 Rodent Liver Transcriptomics Study Researchers investigate the changes in gene expression patterns in mice flown on STS-135 using transcription profiling methods
liver section
Coherent anti-Stokes Raman scattering spectroscopy of liver from mice flown aboard STS-135 compared with AEM ground controls show significantly more lipid accumulation, consistent with the up regulation of genes involved in triglyceride biosynthesis and lipid droplet formation measured in the flight mice.

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.

  • Study Title: STS-135 Liver Transcriptomics
  • Principal Investigator: Dr. Michael Pecaut
  • Organism: Rodent
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
New Data Available on the GeneLab Data System: Researchers Compare International Space Station Environmental Microbiome with That of Earth-Based Cleanrooms Researchers use whole genome sequencing methods to investigate whether the viable microbiome associated with the International Space Station varies from the viable microbiomes of cleanrooms on Earth
diagram of taxonomic profiles
Hierarchical clustering of samples using taxonomic profiles at the genus level. The taxonomic profiles are clustered based on sampling location. The color scale reflects log-normalized proportional values (e.g. - 1~10%, -2~1%, -3~0.1%). Rows and columns are clustered independently using the furthest neighbor algorithm with a Euclidean distance metric. o: order; f: family; g: genus

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.

  • Study Title: Microbiomes of the Dust Particles Collected from the International Space Station and Spacecraft Assembly Facilities
  • Principal Investigator: Dr. Kasthuri Venkateswaran
  • Organism: Environmental Samples
  • Data Type: DNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Dr. Sarah Wyatt of Ohio University Partners with GeneLab on Arabidopsis RNA and Protein Profiling Study Researchers investigate differences in gene and protein expression in Arabidopsis seedlings when grown in space and on the ground.
photo of deintegration process
Colin Kruse (Ohio University) and Susan Manning-Roach (Kennedy Space Center), in a cold room at Kennedy Space Center, deintegrating the experiment after the spaceflight.

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.

  • Study Title: Proteomics and Transcriptomics Analysis of Arabidopsis Seedlings in Microgravity
  • Principal Investigator: Sarah Wyatt, Ph.D.; Ohio University
  • PI Website Link: wyattlab.wordpress.com
  • Organism: Arabidopsis thaliana
  • Data Type: Mass Spectrometry Assay Data; RNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Dr. Simon Gilroy Partners with GeneLab on the Study of Ecotypic Variation in Plant Transcriptomes Researchers investigate the transcriptional differences of four Arabidopsis ecotypes using RNA sequencing methods
seedlings in petri dish
Seedlings of the Columbia ecotype of Arabidopsis thaliana grown onboard the International Space Station and fixed at 8 days in RNAlater.

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.

  • Study Title: Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes
  • Principal Investigator: Dr. Simon Gilroy; University of Wisconsin - Madison
  • PI Website Link: botany.wisc.edu
  • Organism: Arabidopsis thaliana
  • Data Type: RNA Sequence Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
New Transcription Profiling Data Available on the GeneLab Data System Identification of mechanosensitive genes in osteoblasts by comparative microarray studies using the rotating wall vessel and the random positioning machine

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.

  • Study Title: Transcription profiling of mouse osteoblasts under static vs simulated microgravity
  • Organism: Mus musculus
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Simulation Technique Reveals Delay in the Development of Fruit Flies When Exposed to Microgravity

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.

  • Study Title: Transcription profiling of Drosophila exposed to a levitation magnet for different lengths of time
  • Organism: Drosophila melanogaster
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Researchers use Genechip Technology to Investigate Effects of Microgravity on Murine Bone Marrow Stromal Cells

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.

  • Study Title: Genechip analysis of bone marrow osteoprogenitors exposed to microgravity
  • Principal Investigator: Massimiliano Monticone
  • Organism: Mus musculus
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
Bacillus subtilis Spores Exposed to Real Space Conditions

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.

  • Study Title: Bacillus subtilis spores, PROTECT experiment, Space-exposed and Mars-exposed vs. Earth-control
  • Principal Investigator: Wayne L. Nicholson
  • Organism: Bacillus subtilis
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
October 29, 2015 —
MESSAGE 2 space experiment with Rhodospirillum rubrum S1H

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.

  • Study Title: MESSAGE 2 space experiment with Rhodospirillum rubrum S1H
  • Organism: Rhodospirillum rubrum
  • Data Type: Transcription Profiling Data
  • Study Link: genelab-data.ndc.nasa.gov
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