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Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M. A New Era for Space Life Science: International Standards for Space Omics Processing. Patterns (N Y) 2020; 1:100148. [PMID: 33336201 PMCID: PMC7733874 DOI: 10.1016/j.patter.2020.100148] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance standard guidelines between space biologists at a global level. Here we introduce our consortium and share past lessons learned and future challenges related to spaceflight omics.
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Affiliation(s)
- Lindsay Rutter
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Henry Cope
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Kathleen M. Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mariano I. Gabitto
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Samrawit Gebre
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Stefan J. Green
- Genome Research Core, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sigrid S. Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Nathaniel J. Szewczyk
- Ohio Musculoskeletal and Neurological Institute (OMNI), Ohio University, Athens, OH 45701, USA
| | - Deanne M. Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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Takahashi S, Ohta K, Furubayashi N, Yan B, Koga M, Wada Y, Yamada M, Inaka K, Tanaka H, Miyoshi H, Kobayashi T, Kamigaichi S. JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals. J Synchrotron Radiat 2013; 20:968-73. [PMID: 24121350 PMCID: PMC3795566 DOI: 10.1107/s0909049513021596] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 05/08/2023]
Abstract
The Japan Aerospace Exploration Agency (JAXA) started a high-quality protein crystal growth project, now called JAXA PCG, on the International Space Station (ISS) in 2002. Using the counter-diffusion technique, 14 sessions of experiments have been performed as of 2012 with 580 proteins crystallized in total. Over the course of these experiments, a user-friendly interface framework for high accessibility has been constructed and crystallization techniques improved; devices to maximize the use of the microgravity environment have been designed, resulting in some high-resolution crystal growth. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the ISS, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed. In this article, the current status of JAXA PCG is discussed, and a rational approach to high-quality protein crystal growth in microgravity based on numerical analyses is explained.
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Affiliation(s)
- Sachiko Takahashi
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Kazunori Ohta
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Naoki Furubayashi
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Bin Yan
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Misako Koga
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Yoshio Wada
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Mitsugu Yamada
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Hiroaki Tanaka
- Confocal Science Inc., Hayakawa 2nd Building 7F, 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
- Correspondence e-mail:
| | - Hiroshi Miyoshi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Tomoyuki Kobayashi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Shigeki Kamigaichi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
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Alegana VA, Atkinson PM, Wright JA, Kamwi R, Uusiku P, Katokele S, Snow RW, Noor AM. Estimation of malaria incidence in northern Namibia in 2009 using Bayesian conditional-autoregressive spatial-temporal models. Spat Spatiotemporal Epidemiol 2013; 7:25-36. [PMID: 24238079 PMCID: PMC3839406 DOI: 10.1016/j.sste.2013.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 08/05/2013] [Accepted: 09/05/2013] [Indexed: 10/29/2022]
Abstract
As malaria transmission declines, it becomes increasingly important to monitor changes in malaria incidence rather than prevalence. Here, a spatio-temporal model was used to identify constituencies with high malaria incidence to guide malaria control. Malaria cases were assembled across all age groups along with several environmental covariates. A Bayesian conditional-autoregressive model was used to model the spatial and temporal variation of incidence after adjusting for test positivity rates and health facility utilisation. Of the 144,744 malaria cases recorded in Namibia in 2009, 134,851 were suspected and 9893 were parasitologically confirmed. The mean annual incidence based on the Bayesian model predictions was 13 cases per 1000 population with the highest incidence predicted for constituencies bordering Angola and Zambia. The smoothed maps of incidence highlight trends in disease incidence. For Namibia, the 2009 maps provide a baseline for monitoring the targets of pre-elimination.
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Affiliation(s)
- Victor A Alegana
- Malaria Public Health Department, KEMRI-Wellcome Trust-University of Oxford Collaborative Programme, P.O. Box 43640, 00100 GPO Nairobi, Kenya; Centre for Geographical Health Research, Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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