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Scott A, Willis CR, Muratani M, Higashitani A, Etheridge T, Szewczyk NJ, Deane CS. Caenorhabditis elegans in microgravity: An omics perspective. iScience 2023; 26:107189. [PMID: 37456835 PMCID: PMC10344948 DOI: 10.1016/j.isci.2023.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
The application of omics to study Caenorhabditis elegans (C. elegans) in the context of spaceflight is increasing, illuminating the wide-ranging biological impacts of spaceflight on physiology. In this review, we highlight the application of omics, including transcriptomics, genomics, proteomics, multi-omics, and integrated omics in the study of spaceflown C. elegans, and discuss the impact, use, and future direction of this branch of research. We highlight the variety of molecular alterations that occur in response to spaceflight, most notably changes in metabolic and neuromuscular gene regulation. These transcriptional features are reproducible and evident across many spaceflown species (e.g., mice and astronauts), supporting the use of C. elegans as a model organism to study spaceflight physiology with translational capital. Integrating tissue-specific, spatial, and multi-omics approaches, which quantitatively link molecular responses to phenotypic adaptations, will facilitate the identification of candidate regulatory molecules for therapeutic intervention and thus represents the next frontiers in C. elegans space omics research.
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Affiliation(s)
- Amanda Scott
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Craig R.G. Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | | | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Nathaniel J. Szewczyk
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
- Ohio Musculoskeletal and Neurological Institute, Ohio University, Athens, OH, USA
| | - Colleen S. Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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Kalichamy SS, Alcantara AV, Yoon KH, Lee JI. A Simple Protocol to Analyze the Effects of Simulated Microgravity on Nematodes. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021150097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Deane CS, da Silveira WA, Herranz R. Space omics research in Europe: Contributions, geographical distribution and ESA member state funding schemes. iScience 2022; 25:103920. [PMID: 35265808 PMCID: PMC8898910 DOI: 10.1016/j.isci.2022.103920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The European research community, via European Space Agency (ESA) spaceflight opportunities, has significantly contributed toward our current understanding of spaceflight biology. Recent molecular biology experiments include "omic" analysis, which provides a holistic and systems level understanding of the mechanisms underlying phenotypic adaptation. Despite vast interest in, and the immense quantity of biological information gained from space omics research, the knowledge of ESA-related space omics works as a collective remains poorly defined due to the recent exponential application of omics approaches in space and the limited search capabilities of pre-existing records. Thus, a review of such contributions is necessary to clarify and promote the development of space omics among ESA and ESA state members. To address this gap, in this review, we i) identified and summarized omics works led by European researchers, ii) geographically described these omics works, and iii) highlighted potential caveats in complex funding scenarios among ESA member states.
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Affiliation(s)
- Colleen S Deane
- Department of Sport and Health Science, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK.,Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | | | - Willian A da Silveira
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD, 2080, Malta
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
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Cahill T, Cope H, Bass JJ, Overbey EG, Gilbert R, da Silveira WA, Paul AM, Mishra T, Herranz R, Reinsch SS, Costes SV, Hardiman G, Szewczyk NJ, Tahimic CGT. Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight. Int J Mol Sci 2021; 22:ijms22179470. [PMID: 34502375 PMCID: PMC8430797 DOI: 10.3390/ijms22179470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Bioinformatics approaches have proven useful in understanding biological responses to spaceflight. Spaceflight experiments remain resource intensive and rare. One outstanding issue is how to maximize scientific output from a limited number of omics datasets from traditional animal models including nematodes, fruitfly, and rodents. The utility of omics data from invertebrate models in anticipating mammalian responses to spaceflight has not been fully explored. Hence, we performed comparative analyses of transcriptomes of soleus and extensor digitorum longus (EDL) in mice that underwent 37 days of spaceflight. Results indicate shared stress responses and altered circadian rhythm. EDL showed more robust growth signals and Pde2a downregulation, possibly underlying its resistance to atrophy versus soleus. Spaceflight and hindlimb unloading mice shared differential regulation of proliferation, circadian, and neuronal signaling. Shared gene regulation in muscles of humans on bedrest and space flown rodents suggest targets for mitigating muscle atrophy in space and on Earth. Spaceflight responses of C. elegans were more similar to EDL. Discrete life stages of D. melanogaster have distinct utility in anticipating EDL and soleus responses. In summary, spaceflight leads to shared and discrete molecular responses between muscle types and invertebrate models may augment mechanistic knowledge gained from rodent spaceflight and ground-based studies.
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Affiliation(s)
- Thomas Cahill
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
| | - Henry Cope
- Nottingham Biomedical Research Centre (BRC), School of Computer Science, University of Nottingham, Nottingham NG7 2QL, UK;
| | - Joseph J. Bass
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research (NIHR), Nottingham Biomedical Research Centre (BRC), University of Nottingham, Nottingham NG7 2QL, UK; (J.J.B.); (N.J.S.)
| | - Eliah G. Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Rachel Gilbert
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Universities Space Research Association, Columbia, MD 21046, USA
| | - Willian Abraham da Silveira
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
- Department of Biological Sciences, School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent ST4 2DF, UK
| | - Amber M. Paul
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL 32114, USA
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94305, USA;
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas–CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Sigrid S. Reinsch
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.); (G.H.)
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Nathaniel J. Szewczyk
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research (NIHR), Nottingham Biomedical Research Centre (BRC), University of Nottingham, Nottingham NG7 2QL, UK; (J.J.B.); (N.J.S.)
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Candice G. T. Tahimic
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA; (R.G.); (A.M.P.); (S.S.R.); (S.V.C.)
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
- Correspondence:
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Banerjee A, Roychoudhury A. The gymnastics of epigenomics in rice. PLANT CELL REPORTS 2018; 37:25-49. [PMID: 28866772 DOI: 10.1007/s00299-017-2192-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 05/21/2023]
Abstract
Epigenomics is represented by the high-throughput investigations of genome-wide epigenetic alterations, which ultimately dictate genomic, transcriptomic, proteomic and metabolomic dynamism. Rice has been accepted as the global staple crop. As a result, this model crop deserves significant importance in the rapidly emerging field of plant epigenomics. A large number of recently available data reveal the immense flexibility and potential of variable epigenomic landscapes. Such epigenomic impacts and variability are determined by a number of epigenetic regulators and several crucial inheritable epialleles, respectively. This article highlights the correlation of the epigenomic landscape with growth, flowering, reproduction, non-coding RNA-mediated post-transcriptional regulation, transposon mobility and even heterosis in rice. We have also discussed the drastic epigenetic alterations which are reported in rice plants grown from seeds exposed to the extraterrestrial environment. Such abiotic conditions impose stress on the plants leading to epigenomic modifications in a genotype-specific manner. Some significant bioinformatic databases and in silico approaches have also been explained in this article. These softwares provide important interfaces for comparative epigenomics. The discussion concludes with a unified goal of developing epigenome editing to promote biological hacking of the rice epigenome. Such a cutting-edge technology if properly standardized, can integrate genomics and epigenomics together with the generation of high-yielding trait in several cultivars of rice.
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Affiliation(s)
- Aditya Banerjee
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India.
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Ma L, Ma J, Xu K. Effect of spaceflight on the circadian rhythm, lifespan and gene expression of Drosophila melanogaster. PLoS One 2015; 10:e0121600. [PMID: 25798821 PMCID: PMC4370389 DOI: 10.1371/journal.pone.0121600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/16/2015] [Indexed: 12/20/2022] Open
Abstract
Space travelers are reported to experience circadian rhythm disruption during spaceflight. However, how the space environment affects circadian rhythm is yet to be determined. The major focus of this study was to investigate the effect of spaceflight on the Drosophila circadian clock at both the behavioral and molecular level. We used China's Shenzhou-9 spaceship to carry Drosophila. After 13 days of spaceflight, behavior tests showed that the flies maintained normal locomotor activity rhythm and sleep pattern. The expression level and rhythm of major clock genes were also unaffected. However, expression profiling showed differentially regulated output genes of the circadian clock system between space flown and control flies, suggesting that spaceflight affected the circadian output pathway. We also investigated other physiological effects of spaceflight such as lipid metabolism and lifespan, and searched genes significantly affected by spaceflight using microarray analysis. These results provide new information on the effects of spaceflight on circadian rhythm, lipid metabolism and lifespan. Furthermore, we showed that studying the effect of spaceflight on gene expression using samples collected at different Zeitgeber time could obtain different results, suggesting the importance of appropriate sampling procedures in studies on the effects of spaceflight.
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Affiliation(s)
- Lingling Ma
- Laboratory of Space Microbiology, Shenzhou Space Biotechnology Group, China Academy of Space Technology, Beijing, China
| | - Jun Ma
- Laboratory of Space Microbiology, Shenzhou Space Biotechnology Group, China Academy of Space Technology, Beijing, China
| | - Kanyan Xu
- Laboratory of Space Microbiology, Shenzhou Space Biotechnology Group, China Academy of Space Technology, Beijing, China
- * E-mail:
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Herranz R, Medina FJ. Cell proliferation and plant development under novel altered gravity environments. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16 Suppl 1:23-30. [PMID: 24112664 DOI: 10.1111/plb.12103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/02/2013] [Indexed: 05/11/2023]
Abstract
Gravity is a key factor for life on Earth. It is the only environmental factor that has remained constant throughout evolution, and plants use it to modulate important physiological activities; gravity removal or alteration produces substantial changes in essential functions. For root gravitropism, gravity is sensed in specialised cells, which are capable of detecting magnitudes of the g vector lower than 10(-3) . Then, the mechanosignal is transduced to upper zones of the root, resulting in changes in the lateral distribution of auxin and in the rate of auxin polar transport. Gravity alteration has consequences for cell growth and proliferation rates in root meristems, which are the basis of the developmental programme of a plant, in which regulation via auxin is involved. The effect is disruption of meristematic competence, i.e. the strict coordination between cell proliferation and growth, which characterises meristematic cells. This effect can be related to changes in the transport and distribution of auxin throughout the root. However, similar effects of gravity alteration have been found in plant cell cultures in vitro, in which neither specialised structures for gravity sensing and signal transduction, nor apparent gravitropism have been described. We postulate that gravity resistance, a general mechanism of cellular origin for developing rigid structures in plants capable of resisting the gravity force, could also be responsible for the changes in cell growth and proliferation parameters detected in non-specialised cells. The mechanisms of gravitropism and graviresistance are complementary, the first being mostly sensitive to the direction of the gravity vector, and the second to its magnitude. At a global molecular level, the consequence of gravity alteration is that the genome should be finely tuned to counteract a type of stress that plants have never encountered before throughout evolution. Multigene families and redundant genes present an advantage in that they can experience changes without the risk of being deleterious and, for this reason, they should play a key role in the response to gravitational stress.
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Affiliation(s)
- R Herranz
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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Hammond TG, Stodieck L, Birdsall HH, Becker JL, Koenig P, Hammond JS, Gunter MA, Allen PL. Effects of microgravity on the virulence of Listeria monocytogenes, Enterococcus faecalis, Candida albicans, and methicillin-resistant Staphylococcus aureus. ASTROBIOLOGY 2013; 13:1081-90. [PMID: 24283929 DOI: 10.1089/ast.2013.0986] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To evaluate effects of microgravity on virulence, we studied the ability of four common clinical pathogens--Listeria monocytogenes, methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecalis, and Candida albicans--to kill wild type Caenorhabditis elegans (C. elegans) nematodes at the larval and adult stages. Simultaneous studies were performed utilizing spaceflight, clinorotation in a 2-D clinorotation device, and static ground controls. The feeding rate of worms for killed E. coli was unaffected by spaceflight or clinorotation. Nematodes, microbes, and growth media were separated until exposed to true or modeled microgravity, then mixed and grown for 48 h. Experiments were terminated by paraformaldehyde fixation, and optical density measurements were used to assay residual microorganisms. Spaceflight was associated with reduced virulence for Listeria, Enterococcus, MRSA, and Candida for both larval and adult C. elegans. These are the first data acquired with a direct in vivo assay system in space to demonstrate virulence. Clinorotation reproduced the effects of spaceflight in some, but not all, virulence assays: Candida and Enterococcus were less virulent for larval worms but not adult worms, whereas virulence of MRSA and Listeria were unaffected by clinorotation in tests with both adult and larval worms. We conclude that four common clinical microorganisms are all less virulent in space.
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Affiliation(s)
- Timothy G Hammond
- 1 Durham VA Medical Center, Research and Development Service, Duke University School of Medicine , Durham, North Carolina
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Warren P, Golden A, Hanover J, Love D, Shephard F, Szewczyk NJ. Evaluation of the Fluids Mixing Enclosure System for Life Science Experiments During a Commercial Caenorhabditis elegans Spaceflight Experiment. ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2013; 51:2241-2250. [PMID: 23794777 PMCID: PMC3684985 DOI: 10.1016/j.asr.2013.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Student Spaceflight Experiments Program (SSEP) is a United States national science, technology, engineering, and mathematics initiative that aims to increase student interest in science by offering opportunities to perform spaceflight experiments. The experiment detailed here was selected and flown aboard the third SSEP mission and the first SSEP mission to the International Space Station (ISS). Caenorhabditis elegans is a small, transparent, self-fertilizing hermaphroditic roundworm that is commonly used in biological experiments both on Earth and in Low Earth Orbit. Past experiments have found decreased expression of mRNA for several genes whose expression can be controlled by the FOXO transcription factor DAF-16. We flew a daf-16 mutant and control worms to determine if the effects of spaceflight on C. elegans are mediated by DAF-16. The experiment used a Type Two Fluids Mixing Enclosure (FME), developed by Nanoracks LLC, and was delivered to the ISS aboard the SpaceX Dragon and returned aboard the Russian Soyuz. The short time interval between experiment selection and the flight rendered preflight experiment verification tests impossible. In addition, published research regarding the viability of the FME in life science experiments was not available. The experiment was therefore structured in such a way as to gather the needed data. Here we report that C. elegans can survive relatively short storage and activation in the FME but cannot produce viable populations for post-flight analysis on extended missions. The FME appears to support short-duration life science experiments, potentially on supply or crew exchange missions, but not on longer ISS expeditions. Additionally, the flown FME was not properly activated, reportedly due to a flaw in training procedures. We suggest that a modified transparent FME could prevent similar failures in future flight experiments.
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Affiliation(s)
- Paul Warren
- Henry E. Lackey High School, 3000 Chicamuxen Road, Indian Head, MD 20640, USA
| | - Andy Golden
- Laboratories of Biochemistry and Genetics and of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - John Hanover
- Laboratories of Biochemistry and Genetics and of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dona Love
- Laboratories of Biochemistry and Genetics and of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Freya Shephard
- Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Nathaniel J. Szewczyk
- Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
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Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ. Spaceflight transcriptomes: unique responses to a novel environment. ASTROBIOLOGY 2012; 12:1-2. [PMID: 22221117 DOI: 10.1089/ast.2011.0745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The spaceflight environment presents unique challenges to terrestrial biology, including but not limited to the direct effects of gravity. As we near the end of the Space Shuttle era, there remain fundamental questions about the response and adaptation of plants to orbital spaceflight conditions. We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity.
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Affiliation(s)
- Anna-Lisa Paul
- Horticultural Sciences and Genetics Institute, University of Florida, Gainesville, Florida, USA
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12
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Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ. Spaceflight transcriptomes: unique responses to a novel environment. ASTROBIOLOGY 2012; 12:40-56. [PMID: 22221117 PMCID: PMC3264962 DOI: 10.1089/ast.2011.0696] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 10/08/2011] [Indexed: 05/20/2023]
Abstract
The spaceflight environment presents unique challenges to terrestrial biology, including but not limited to the direct effects of gravity. As we near the end of the Space Shuttle era, there remain fundamental questions about the response and adaptation of plants to orbital spaceflight conditions. We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity.
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Affiliation(s)
- Anna-Lisa Paul
- Horticultural Sciences and Genetics Institute, University of Florida, Gainesville, Florida
| | | | | | | | - Yijun Sun
- University of Florida, Gainesville, Florida
| | | | | | | | | | - Robert J. Ferl
- Interdisciplinary Center for Biotechnology and Research, Horticultural Sciences and Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida
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Oczypok EA, Etheridge T, Freeman J, Stodieck L, Johnsen R, Baillie D, Szewczyk NJ. Remote automated multi-generational growth and observation of an animal in low Earth orbit. J R Soc Interface 2011; 9:596-9. [PMID: 22130552 PMCID: PMC3262433 DOI: 10.1098/rsif.2011.0716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The ultimate survival of humanity is dependent upon colonization of other planetary bodies. Key challenges to such habitation are (patho)physiologic changes induced by known, and unknown, factors associated with long-duration and distance space exploration. However, we currently lack biological models for detecting and studying these changes. Here, we use a remote automated culture system to successfully grow an animal in low Earth orbit for six months. Our observations, over 12 generations, demonstrate that the multi-cellular soil worm Caenorhabditis elegans develops from egg to adulthood and produces progeny with identical timings in space as on the Earth. Additionally, these animals display normal rates of movement when fully fed, comparable declines in movement when starved, and appropriate growth arrest upon starvation and recovery upon re-feeding. These observations establish C. elegans as a biological model that can be used to detect changes in animal growth, development, reproduction and behaviour in response to environmental conditions during long-duration spaceflight. This experimental system is ready to be incorporated on future, unmanned interplanetary missions and could be used to study cost-effectively the effects of such missions on these biological processes and the efficacy of new life support systems and radiation shielding technologies.
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Affiliation(s)
- Elizabeth A Oczypok
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Adenle AA, Johnsen B, Szewczyk NJ. Review of the results from the International C. elegans first experiment (ICE-FIRST). ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2009; 44:210-216. [PMID: 20161164 PMCID: PMC2719817 DOI: 10.1016/j.asr.2009.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In an effort to speed the rate of discovery in space biology and medicine NASA introduced the now defunct model specimen program. Four nations applied this approach with C. elegans in the ICE-FIRST experiment. Here we review the standardized culturing as well as the investigation of muscle adaptation, space biology radiation, and gene expression in response to spaceflight. Muscle studies demonstrated that decreased expression of myogenic transcription factors underlie the decreased expression of myosin seen in flight, a response that would appear to be evolutionarily conserved. Radiation studies demonstrated that radiation damaged cells should be able to be removed via apoptosis in flight, and that C. elegans can be employed as a biological accumulating dosimeter. Lastly, ICE-FIRST gave us our first glimpse at the genomic response to spaceflight, suggesting that altered Insulin and/or TGF-beta signaling in-flight may underlie many of the biological changes seen in response to spaceflight. The fact that the results obtained with C. elegans appear to have strong similarities in human beings suggests that not only will C. elegans prove an invaluable model for understanding the fundamental biological changes seen during spaceflight but that it may also be invaluable for understanding those changes associated with human health concerns in space.
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Affiliation(s)
- A A Adenle
- University of Nottingham, School of Graduate Entry Medicine and Health, Derby, DE22 3DT, United Kingdom
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Ou X, Long L, Zhang Y, Xue Y, Liu J, Lin X, Liu B. Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.). Mutat Res 2008; 662:44-53. [PMID: 19135069 DOI: 10.1016/j.mrfmmm.2008.12.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2008] [Revised: 12/03/2008] [Accepted: 12/05/2008] [Indexed: 11/29/2022]
Abstract
Spaceflight represents a complex environmental condition in which several interacting factors such as cosmic radiation, microgravity and space magnetic fields are involved, which may provoke stress responses and jeopardize genome integrity. Given the inherent property of epigenetic modifications to respond to intrinsic as well as external perturbations, it is conceivable that epigenetic markers like DNA methylation may undergo alterations in response to spaceflight. We report here that extensive alteration in both DNA methylation and gene expression occurred in rice plants subjected to a spaceflight, as revealed by a set of characterized sequences including 6 transposable elements (TEs) and 11 cellular genes. We found that several features characterize the alterations: (1) All detected alterations are hypermethylation events; (2) whereas alteration in both CG and CNG methylation occurred in the TEs, only alteration in CNG methylation occurred in the cellular genes; (3) alteration in expression includes both up- and down-regulations, which did not show a general correlation with alteration in methylation; (4) altered methylation patterns in both TEs and cellular genes are heritable to progenies at variable frequencies; however, stochastic reversion to wild-type patterns and further de novo changes in progenies are also apparent; and (5) the altered expression states in both TEs and cellular genes are also heritable to selfed progenies but with markedly lower transmission frequencies than altered DNA methylation states. Furthermore, we found that a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, the SWI/SNF chromatin remodeller (DDM1) and siRNA-related proteins are extremely sensitive to perturbation by spaceflight, which might be an underlying cause for the altered methylation patterns in the space-flown plants. We discuss implications of spaceflight-induced epigenetic variations with regard to health safety issues of spaceship crews and potentiality of spaceflight as a means for mutagenesis in crop breeding.
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Affiliation(s)
- Xiufang Ou
- Key Laboratory of Molecular Epigenetic of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
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Szewczyk N, Tillman J, Conley C, Granger L, Segalat L, Higashitani A, Honda S, Honda Y, Kagawa H, Adachi R, Higashibata A, Fujimoto N, Kuriyama K, Ishioka N, Fukui K, Baillie D, Rose A, Gasset G, Eche B, Chaput D, Viso M. Description of International Caenorhabditis elegans Experiment first flight (ICE-FIRST). ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2008; 42:1072-1079. [PMID: 22146801 PMCID: PMC2493420 DOI: 10.1016/j.asr.2008.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Traveling, living and working in space is now a reality. The number of people and length of time in space is increasing. With new horizons for exploration it becomes more important to fully understand and provide countermeasures to the effects of the space environment on the human body. In addition, space provides a unique laboratory to study how life and physiologic functions adapt from the cellular level to that of the entire organism. Caenorhabditis elegans is a genetic model organism used to study physiology on Earth. Here we provide a description of the rationale, design, methods, and space culture validation of the ICE-FIRST payload, which engaged C. elegans researchers from four nations. Here we also show C. elegans growth and development proceeds essentially normally in a chemically defined liquid medium on board the International Space Station (10.9 day round trip). By setting flight constraints first and bringing together established C. elegans researchers second, we were able to use minimal stowage space to successfully return a total of 53 independent samples, each containing more than a hundred individual animals, to investigators within one year of experiment concept. We believe that in the future, bringing together individuals with knowledge of flight experiment operations, flight hardware, space biology, and genetic model organisms should yield similarly successful payloads.
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Affiliation(s)
- N.J. Szewczyk
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
- School of Graduate Entry Medicine and Health, University of Nottingham, Derby City Hospital, Derby DE22 3DT, UK
- Corresponding author. Address: School of Graduate Entry Medicine and Health, University of Nottingham, Derby City Hospital, Derby DE22 3DT, UK. Tel.: +44 1332 724615. E-mail address: (N.J. Szewczyk)
| | - J. Tillman
- Lockheed Martin, Moffett Field, CA 94035, USA
| | - C.A. Conley
- National Aeronautics and Space Administration, Moffett Field, CA 94035, USA
| | - L. Granger
- CGMC, CNRS-UMR 5534, Universite Lyon1, 43 bld du 11 Novembre, 69622 Villeurbanne Cedex, France
| | - L. Segalat
- CGMC, CNRS-UMR 5534, Universite Lyon1, 43 bld du 11 Novembre, 69622 Villeurbanne Cedex, France
| | - A. Higashitani
- Graduate School of Life Sciences, Tohoku University, Sendai 980−8557, Japan
| | - S. Honda
- Tokyo Metropolitan Institute of Gerontology, Tokyo 173−0015, Japan
| | - Y. Honda
- Tokyo Metropolitan Institute of Gerontology, Tokyo 173−0015, Japan
| | - H. Kagawa
- Graduate School of Natural Science and Technology, Okayama University, 3−1−1, Tsushima Naka, Okayama City 700−8530, Japan
| | - R. Adachi
- Graduate School of Natural Science and Technology, Okayama University, 3−1−1, Tsushima Naka, Okayama City 700−8530, Japan
| | - A. Higashibata
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - N. Fujimoto
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - K. Kuriyama
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - N. Ishioka
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - K. Fukui
- Japan Space Forum, Tokyo 100−0004, Japan
| | - D. Baillie
- University of British Columbia, Vancouver, BC, Canada
| | - A. Rose
- University of British Columbia, Vancouver, BC, Canada
| | - G. Gasset
- Groupement Scientifique en Biologie et Medecine Spatiales, Universite Paul Sabatier, 31062 Toulouse Cedex, France
| | - B. Eche
- Groupement Scientifique en Biologie et Medecine Spatiales, Universite Paul Sabatier, 31062 Toulouse Cedex, France
| | - D. Chaput
- Centre National d'Estudes Spatiales, Paris Cedex 01, France
| | - M. Viso
- Centre National d'Estudes Spatiales, Paris Cedex 01, France
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Selch F, Higashibata A, Imamizo-Sato M, Higashitani A, Ishioka N, Szewczyk NJ, Conley CA. Genomic response of the nematode Caenorhabditis elegans to spaceflight. ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2008; 41:807-815. [PMID: 18392117 PMCID: PMC2288577 DOI: 10.1016/j.asr.2007.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
On Earth, it is common to employ laboratory animals such as the nematode Caenorhabditis elegans to help understand human health concerns. Similar studies in Earth orbit should help understand and address the concerns associated with spaceflight. The "International Caenorhabditis elegans Experiment FIRST" (ICE FIRST), was carried out onboard the Dutch Taxiflight in April of 2004 by an international collaboration of laboratories in France, Canada, Japan and the United States. With the exception of a slight movement defect upon return to Earth, the result of altered muscle development, no significant abnormalities were detected in spaceflown C. elegans. Work from Japan revealed apoptosis proceeds normally and work from Canada revealed no significant increase in the rate of mutation. These results suggest that C. elegans can be used to study non-lethal responses to spaceflight and can possibly be developed as a biological sensor. To further our understanding of C. elegans response to spaceflight, we examined the gene transcription response to the 10 days in space using a near full genome microarray analysis. The transcriptional response is consistent with the observed normal developmental timing, apoptosis, DNA repair, and altered muscle development. The genes identified as altered in response to spaceflight are enriched for genes known to be regulated, in C. elegans, in response to altered environmental conditions (Insulin and TGF-beta regulated). These results demonstrate C. elegans can be used to study the effects of altered gravity and suggest that C. elegans responds to spaceflight by altering the expression of at least some of the same metabolic genes that are altered in response to differing terrestrial environments.
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Affiliation(s)
- Florian Selch
- Ames Research Center, National Aeronautics and Space Administration, M/S 239-11, Moffett Field, CA 94035-1000, USA
- Department of Molecular Cell Biology, University of Vienna, A-1010 Vienna, Austria
| | - Akira Higashibata
- Japan Aerospace Exploration Agency, 2-1-1, Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Mari Imamizo-Sato
- Advanced Engineering Services Co., Ltd., Tsukuba Mitsui Building, 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | | | - Noriaki Ishioka
- Japan Aerospace Exploration Agency, 2-1-1, Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Nathaniel J. Szewczyk
- Ames Research Center, National Aeronautics and Space Administration, M/S 239-11, Moffett Field, CA 94035-1000, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
- School of Graduate Entry Medicine and Health, University of Nottingham, Derby DE22 3DT, UK
- * Corresponding author. Address: School of Graduate Entry Medicine and Health, University of Nottingham, Derby DE22 3DT, UK Tel.: +44 1332 724615. E-mail address: (N.J. Szewczyk)
| | - Catharine A. Conley
- Ames Research Center, National Aeronautics and Space Administration, M/S 239-11, Moffett Field, CA 94035-1000, USA
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