Agent-based model for microbial populations exposed to radiation (AMMPER) simulates yeast growth for deep-space experiments
By:
References
- Straume T, Slaba TC, Bhattacharya S, Braby LA. Cosmic-ray interaction data for designing biological experiments in space. Life Sci Space Res. 2017;13:51–59. doi:10.1016/j.lssr.2017.04.002
- Horneck G, Klaus DM, Mancinelli RL. Space Microbiology. Microbiol Mol Biol Rev. 2010;74:121–156. doi:10.1128/MMBR.00016-09
- Afshinnekoo E, Scott RT, MacKay MJ, Pariset E, Cekanaviciute E, Barker R, Gilroy S, Hassane D, Smith SM, Zwart SR, Nelman-Gonzalez M, Crucian BE, Ponomarev SA, Orlov OI, Shiba D, Muratani M, Yamamoto M, Richards SE, Vaishampayan PA, Meydan C, Foox J, Myrrhe J, Istasse E, Singh N, Venkateswaran K, Keune JA, Ray HE, Basner M, Miller J, Vitaterna MH, Taylor DM, Wallace D, Rubins K, Bailey SM, Grabham P, Costes SV, Mason CE, Beheshti A. Fundamental biological features of spaceflight: Advancing the field to enable deep-space exploration. Cell. 2020;183:1162–1184. doi:10.1016/j.cell.2020.10.050
- Furukawa S, Nagamatsu A, Nenoi M, Fujimori A, Kakinuma S, Katsube T, Wang B, Tsuruoka C, Shirai T, Nakamura AJ, Sakaue-Sawano A, Miyawaki A, Harada H, Kobayashi M, Kobayashi J, Kunieda T, Funayama T, Suzuki M, Miyamoto T, Hidema J, Yoshida Y, Takahashi A. Space radiation biology for “Living in Space.” BioMed Res Int. 2020:e4703286. doi:10.1155/2020/4703286
- Montesinos CA, Khalid R, Cristea O, Greenberger JS, Epperly MW, Lemon JA, Boreham DR, Popov D, Gorthi G, Ramkumar N, Jones JA. Space radiation protection countermeasures in microgravity and planetary exploration. Life. 2021;11:829. doi:10.3390/life11080829
- NASA LBLEO Science Working Group. 2018. Life Beyond Low Earth Orbit. Report of a science working group to the NASA Human Exploration and Operations Mission Directorate and Space Life and Physical Sciences Division.
- Blaber E, Boothby T, Carr CE, Everroad RC, Foster J, Galazka J, Lee JA, Lera M, Ricco A, Sanders L, Szewczyk N, Tahimic C, Todd P, Vaishampayan P, Vanapalli S, Zhang Y, Zitnik M, Harrison L. NASA Space Biology Beyond LEO Instrumentation & Science Series Science Working Group 2022 Annual Report. 2023 (No. ntrs. nasa.gov/citations/20230008417).
- Chancellor J, Nowadly C, Williams J, Aunon-Chancellor S, Chesal M, Looper J, Newhauser W. Everything you wanted to know about space radiation but were afraid to ask. J Environ Sci Health Part C Toxicol Carcinog. 2021;39:113–128. doi:10.1080/26896583.2021.1897273
- Coulombe JV, Harrisson G, Lewis BJ, El-Jaby S. Evolving radiological protection guidelines for exploration-class missions. Life Sci Space Res. 2022;doi:10.1016/j.lssr.2022.08.004
- Everroad RC, Foster J, Galazka JM, Jansson J, Lee JA, Lera MP, Perera I, Ricco A, Szewczyk N, Todd P, Zhang Y, Harrison L. NASA Space Biology Beyond LEO Instrumentation & Science Series - Science Working Group 2021 Annual Report. 2021. (No. ntrs. nasa.gov/citations/20210023324).
- Restier-Verlet J, El-Nachef L, Ferlazzo ML, Al-Choboq J, Granzotto A, Bouchet A, Foray N. Radiation on Earth or in space: what does it change? Int J Mol Sci. 2021;22. doi:10.3390/ijms22073739
- Mars K. 5 Hazards of Human Spaceflight. NASA. 2018;
http://www.nasa.gov/hrp/5-hazards-of-human-spaceflight - Ball N, Kagawa H, Hindupur A, Kostakis A, Hogan J, Villanueva A, Sharif S, Donovan F, Settles M, Sims K, Gresser A. 2021. BioNutrients-2: Improvements to the BioNutrients-1 nutrient production system. 50th International Conference on Environmental Systems. ICES-2021-331.
- Ball N, Kagawa H, Hindupur A, Sims K. 2020. BioNutrients-1: Development of an on-demand nutrient production system for long-duration missions.49th International Conference on Environmental Systems. ICES-2020-119. Presented at the 49th International Conference on Environmental Systems.
- Bijlani S, Stephens E, Singh NK, Venkateswaran K, Wang CCC. Advances in space microbiology. iScience. 2021;24:102395. doi:10.1016/j.isci.2021.102395
- Santomartino R, Zea L, Cockell CS. The smallest space miners: principles of space biomining. Extremophiles. 2022;26:7. doi:10.1007/s00792-021-01253-
- Massaro Tieze S, Liddell LC, Santa Maria SR, Bhattacharya S. BioSentinel: A biological CubeSat for deep space exploration. Astrobiology. 2020. doi:10.1089/ast.2019.2068
- Ricco AJ, Maria SRS, Hanel RP, Bhattacharya S. BioSentinel: A 6U nanosatellite for deep-space biological science. IEEE Aerosp Electron Syst Mag. 2020;35:6–18. doi:10.1109/MAES.2019.2953760
- Santa Maria SR, Marina DB, Massaro Tieze S, Liddell LC, Bhattacharya S. BioSentinel: Long-term Saccharomyces cerevisiae preservation for a deep space biosensor mission. Astrobiology. 2020;20:1–14. doi:10.1089/ast.2019.2073
- Bücker H. 1975. Biostack: a study of the biological effects on HZE galactic cosmic radiation. Biomedical Results of Apollo, NASA SP-368. National Aeronautics and Space Administration.
- Cucinotta FA, Wilson JW, Katz R, Atwell W, Badhwar GD, Shavers MR. Track structure and radiation transport model for space radiobiology studies. Adv Space Res. Proceedings of the F3.1, F3.4, F2.4 and F3.8 Symposia of COSPAR Scientific Commission F. 1996;18:183–194. doi:10.1016/0273-1177(96)00039-7
- Mileikowsky C, Cucinotta FA, Wilson JW, Gladman B, Horneck G, Lindegren L, Melosh J, Rickman H, Valtonen M, Zheng JQ. Natural transfer of viable microbes in space. Icarus. 2000;145:391–427. doi:10.1006/icar.1999.6317
- Zea L, Santa Maria SR, Ricco AJ. 7 - CubeSats for microbiology and astrobiology research In: Cappelletti C, Battistini S, Malphrus BK, editors. Cubesat Handbook. Academic Press; 2021. pp. 147–162. doi:10.1016/B978-0-12-817884-3.00007-2
- Kitts C, Ronzano K, Rasay R, Mas I, Williams P, Mahacek P, Minelli G, Hines J, Agasid E, Friedericks C, Piccini M, Parra M, Timucin L, Beasley C, Henschke M, Luzzi E, Mai N, McIntyre M, Ricks R, Squires D, Storment C, Tucker J, Yost B, Defouw G, Ricco A. Flight results from the GeneSat-1 biological microsatellite mission. Small Satell Conf. 2007.
- Minelli G, Kitts C, Ronzano K, Beasley C, Rasay R, Mas I, Williams P, Mahacek P, Shepard J, Acain J, Hines J, Agasid E, Friedericks C, Piccini M, Parra M, Timucin L, Henschke M, Luzzi E, Mai N, McIntyre M, Ricks R, Squires D, Storment C, Tucker J, Yost B, Defouw G, Ricco A. 2008. Extended life flight results from the GeneSat-1 biological microsatellite mission. Small Satellite Conference.
- Padgen MR, Liddell LC, Bhardwaj SR, Gentry D, Marina D, Parra M, Boone T, Tan M, Ellingson L, Rademacher A, Benton J, Schooley A, Mousavi A, Friedericks C, Hanel RP, Ricco AJ, Bhattacharya S, Maria SRS. BioSentinel: A biofluidic nanosatellite monitoring microbial growth and activity in deep space. Astrobiology. 2021;23. doi:10.1089/ast.2020.2305
- Ricco AJ, Parra M, Niesel D, Piccini M, Ly D, McGinnis M, Kudlicki A, Hines JW, Timucin L, Beasley C, Ricks R, McIntyre M, Friedericks C, Henschke M, Leung R, Diaz-Aguado M, Kitts C, Mas I, Rasay M, Agasid E, Luzzi E, Ronzano K, Squires D, Yost B. 2011. PharmaSat: drug dose response in microgravity from a free-flying integrated biofluidic/optical culture-and-analysis satellite. Presented at the Microfluidics, BioMEMS, and Medical Microsystems IX. International Society for Optics and Photonics. p. 79290T. doi:10.1117/12.881082
- Liddell LC, Gentry DM, Gilbert R, Marina D, Massaro Tieze S, Padgen MR, Akiyama K, Keenan K, Bhattacharya S, Santa Maria SR. BioSentinel: validating sensitivity of yeast biosensors to deep space relevant radiation. Astrobiology. 2023;23:648–656. doi:10.1089/ast.2022.0124
- Figliozzi G. 2023. What is the lunar explorer instrument for space biology applications? NASA.
http://www.nasa.gov/ames/leia - Kiefer J. The physical basis for the biological action of heavy ions. New J Phys. 2008;10:075004. doi:10.1088/1367-2630/10/7/075004
- Hellweger FL, Bucci V. 2009. A bunch of tiny individuals—individual-based modeling for microbes. Ecol Model. 2009;220:8–22. doi:10.1016/j.ecolmodel.2008.09.004
- Hellweger FL, Kianirad E. 2007. Individual-based modeling of phytoplankton: Evaluating approaches for applying the cell quota model. J Theor Biol. 2007;249:554–565 doi:10.1016/j.jtbi.2007.08.020
- Plante I, Wu H. 2014. RITRACKS: A software for simulation of stochastic radiation track structure, micro and nanodosimetry, radiation chemistry and DNA damage for heavy ions. Presented at the COSPAR Scientific Assembly. Moscow.
- Blyth BJ, Sykes PJ. Radiation-induced bystander effects: What are they, and how relevant are they to human radiation exposures? Radiat Res. 2011;176:139–157. doi:10.1667/RR2548.1
- Heeran AB, Berrigan HP, O’Sullivan J. The radiation-induced bystander effect (RIBE) and its connections with the hallmarks of cancer. Radiat Res. 2019;192:668–679. doi:10.1667/RR15489.1
- Hei TK, Zhou H, Ivanov VN, Hong M, Lieberman HB, Brenner DJ, Amundson SA, Geard CR. Mechanism of radiation-induced bystander effects: a unifying model. J Pharm Pharmacol. 2005;60:943–950. doi:10.1211/jpp.60.8.0001
- Singh A. 2023. AMMPER. Available at
https://github.com/nasa/AMMPER . - Jorgensen P, Edgington NP, Schneider BL, Rupeš I, Tyers M, Futcher B. The size of the nucleus increases as yeast cells grow. Mol Biol Cell. 2007;18:3523–3532. doi:10.1091/mbc.e06-10-0973
- Krawczyk K, Dzwinel W, Yuen DA. Nonlinear development of bacterial colony modeled with cellular automata and agent objects. Int J Mod Phys C. 2003;14:1385–1404. doi:10.1142/S0129183103006199
- Horowitz J, Normand MD, Corradini MG, Peleg M. Probabilistic model of microbial cell growth, division, and mortality. Appl Environ Microbiol. 2010;76:230–242. doi:10.1128/AEM.01527-09
- Allen RJ, Waclaw B. Bacterial growth: a statistical physicist’s guide. Rep Prog Phys. 2029;82:016601. doi:10.1088/1361-6633/aae546
- Simonsen LC, Slaba TC, Guida P, Rusek A. NASA’s first ground-based galactic cosmic ray simulator: Enabling a new era in space radiobiology research. PLOS Biol. 2020;18:e3000669. doi:10.1371/journal.pbio.3000669
- Curtis SB, Letaw JR. Galactic cosmic rays and cell-hit frequencies outside the magnetosphere. Adv Space Res. 1989;9:293–298. doi:10.1016/0273-1177(89)90452-3
- Kim M-HY, Rusek A, Cucinotta FA. Issues for simulation of galactic cosmic ray exposures for radiobiological research at ground-based accelerators. Front Oncol. 2015;5.
- Stewart RD, Yu VK, Georgakilas AG, Koumenis C, Park JH, Carlson DJ. Effects of radiation quality and oxygen on clustered DNA lesions and cell death. Radiat Res. 2011;176:587–602. doi:10.1667/RR2663.1
- Wingate CL, Baum JW. Measured radial distributions of dose and LET for alpha and proton beams in hydrogen and tissue-equivalent gas. Radiat Res. 1976;65:1–19. doi:10.2307/3574282
- Ferradini C, Jay-Gerin J-P. The effect of pH on water radiolysis: a still open question — a minireview. Res Chem Intermed. 2000;26:549–565. doi:10.1163/156856700X00525
- Attri P, Kim YH, Park DH, Park JH, Hong YJ, Uhm HS, Kim K-N, Fridman A, Choi EH. Generation mechanism of hydroxyl radical species and its lifetime prediction during the plasma-initiated ultraviolet (UV) photolysis. Sci Rep. 2015;5:9332. doi:10.1038/srep09332
- Krumova K, Cosa G. Overview of reactive oxygen species. Singlet Oxygen: Applications in Biosciences and Nanosciences, Comprehensive Series in Photochemical & Photobiological Sciences. London: Royal Society of Chemistry; 2016, 1–12.
- Plante I, Cucinotta F. Simulation of the radiolysis of water using Green’s functions of the diffusion equation. Radiat Prot Dosimetry. 2015;166. doi:10.1093/rpd/ncv179
- Thomas JK. Rates of reaction of the hydroxyl radical. Trans Faraday Soc. 1965;61:702. doi:10.1039/tf9656100702
- Le Caër S. 2011. Water radiolysis: influence of oxide surfaces on H2 production under ionizing radiation. Water. 2011;3:235–253. doi:10.3390/w3010235
- Cucinotta FA, Wilson JW, Katz R, Atwell W, Badhwar GD, Shavers MR. Track structure and radiation transport model for space radiobiology studies. Adv Space Res. Proceedings of the F3.1, F3.4, F2.4 and F3.8 Symposia of COSPAR Scientific Commission F. 1996;18:183–194. doi:10.1016/0273-1177(96)00039-7
- Nikjoo H, O’Neill P, Terrissol M, Goodhead DT. Quantitative modelling of DNA damage using Monte Carlo track structure method. Radiat Environ Biophys. 1999;38:31–38. doi:10.1007/s004110050135
- Erixon K, Cedervall B. Linear induction of DNA double-strand breakage with X-ray dose, as determined from DNA fragment size distribution. Radiat Res. 1995;142:153–162. doi:10.2307/3579023
- Ponomarev AL, George K, Cucinotta FA. Computational model of chromosome aberration yield induced by high- and low-LET radiation exposures. Radiat Res. 2012;177:727–737. doi:10.1667/RR2659.1
- Madeo F, Fröhlich E, Ligr M, Grey M, Sigrist SJ, Wolf DH, Fröhlich K-U. Oxygen stress: a regulator of apoptosis in yeast. J Cell Biol. 1999;145:757–767. doi:10.1083/jcb.145.4.757
- Karschau J, de Almeida C, Richard MC, Miller S, Booth IR, Grebogi C, de Moura APS. A matter of life or death: modeling DNA damage and repair in bacteria. Biophys J. 2011;100:814–821. doi:10.1016/j.bpj.2010.12.3713
- Lisby M, Mortensen UH, Rothstein R. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat Cell Biol. 2003;5:572–577. doi:10.1038/ncb997
- Plante I, Slaba T, Shavers Z, Hada M. A bi-exponential repair algorithm for radiation-induced double-strand breaks: application to simulation of chromosome aberrations. Genes. 2019;10:936. doi:10.3390/genes10110936
- Lettier G, Feng Q, Mayolo AA de, Erdeniz N, Reid RJD, Lisby M, Mortensen UH, Rothstein R. The role of DNA double-strand breaks in spontaneous homologous recombination in S. cerevisiae. PLOS Genet. 2006;2:e194. doi:10.1371/journal.pgen.0020194
- Kiefer J, Egenolf R, Ikpeme S. Heavy ion-induced DNA double-strand breaks in yeast. Radiat Res. 2002;157:141–148. doi:10.1667/0033-7587(2002)157[0141:HIIDDS]2.0.CO;2
- Kost M, Kiefer J. Biological action of heavy ion irradiation on individual yeast cells In: McCormack PD, Swenberg CE, Bücker H, editors. Terrestrial Space Radiation and Its Biological Effects, Nato ASI Series. Boston, MA: Springer US; 1988, 197–203. doi:10.1007/978-1-4613-1567-4_14
- Kiefer J, Müller J, Götzen J. 1988. Mitotic recombination in continuously γ-irradiated diploid yeast. Radiat Res. 1988;113:71–78. doi:10.2307/3577181
- Kiefer J, Wagner E. Radiosensitivity of continuous cultures: experiments with diploid yeast. Radiat Res. 1975;63:336–345. doi:10.2307/3574158
- Nicholson WL, Ricco AJ. Nanosatellites for biology in space: in situ measurement of Bacillus subtilis spore germination and growth after 6 months in low Earth orbit on the O/OREOS Mission. Life. 2020;10:1. doi:10.3390/life10010001
- Padgen MR, Lera MP, Parra MP, Ricco AJ, Chin M, Chinn TN, Cohen A, Friedericks CR, Henschke MB, Snyder TV, Spremo SM, Wang J-H, Matin AC. EcAMSat spaceflight measurements of the role of σs in antibiotic resistance of stationary phase Escherichia coli in microgravity. Life Sci Space Res. 2020;24:18–24. doi:10.1016/j.lssr.2019.10.007
- Pross HD, Casares A, Kiefer J. Induction and repair of DNA double-strand breaks under irradiation and microgravity. Radiat Res. 153:521–525. doi:10.1667/0033-7587(2000)153[0521:IARODD]2.0.CO;2
- Pross HD, Kiefer J. Repair of cellular radiation damage in space under microgravity conditions. Radiat Environ Biophys. 1999;38:133–138. doi:10.1007/s004110050149
- Takahashi A, Ohnishi K, Takahashi S, Masukawa M, Sekikawa K, Amano T, Nakano T, Nagaoka S, Ohnishi T. The effects of microgravity on induced mutation in Escherichia coli and Saccharomyces cerevisiae. Adv Space Res. 2001;28:555–561. doi:10.1016/S0273-1177(01)00391-X
- Ware JH, Sanzari J, Avery S, Sayers C, Krigsfeld G, Nuth M, Wan XS, Rusek A, Kennedy AR. Effects of proton radiation dose, dose rate and dose fractionation on hematopoietic cells in mice. Radiat Res. 2010;174:325–330. doi:10.1667/RR1979.1
- Bujarrabal A, Schumacher B. 2016. Hormesis running hot and cold. Cell Cycle. 2016;15(24);3335–3336. doi: 10.1080/15384101.2016.1235859
- Calabrese E.J. Hormetic mechanisms. Crit Rev Toxicol. 2013;43:580–606. doi:10.3109/10408444.2013.808172
- Kabilan U, Graber TE, Alain T, Klokov D. 2020. Ionizing radiation and translation control: a link to radiation hormesis? Int J Mol Sci. 2020;21:6650. doi:10.3390/ijms21186650
- Mathieu A, Fleurier S, Frénoy A, Dairou J, Bredeche M-F, Sanchez-Vizuete P, Song X, Matic I. Discovery and function of a general core hormetic stress response in E. coli induced by sublethal concentrations of antibiotics. Cell Rep. 2016;17:46–57. doi:10.1016/j.celrep.2016.09.001
- Vaiserman AM. Radiation hormesis: historical perspective and implications for low-dose cancer risk assessment. Dose-Response 2010;8. doi:10.2203/dose-response.09-037.Vaiserman
- Keszenman DJ, Sutherland BM. Yields of clustered DNA damage induced by charged-particle radiations of similar kinetic energy per nucleon: LET dependence in different DNA microenvironments. Radiat Res. 2010;174:238–250. doi:10.1667/RR2093.1
- Li Y, Reynolds P, O’Neill P, Cucinotta FA. Modeling damage complexity-dependent non-homologous end-joining repair pathway. PLOS ONE. 2014;9:e85816. doi:10.1371/journal.pone.0085816
- Lomax ME, Folkes LK, O’Neill P. Biological consequences of radiation-induced DNA damage: relevance to radiotherapy. Clin Oncol. Adv Clin Radiobiol. 2013;25:578–585. doi:10.1016/j.clon.2013.06.007
- Moscariello M, Sutherland B. Saccharomyces cerevisiae-based system for studying clustered DNA damages. Radiat Environ Biophys. 2010;49:447–456. doi:10.1007/s00411-010-0303-3
- Friedland W, Dingfelder M, Kundrát P, Jacob P. Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. Mutat Res Mol Mech Mutagen 2911;711:28–40. doi:10.1016/j.mrfmmm.2011.01.003
- Prise KM, Schettino G, Folkard M, Held KD. New insights on cell death from radiation exposure. Lancet Oncol. 2005;6:520–528. doi:10.1016/S1470-2045(05)70246-1
- Harper JV, Anderson JA, O’Neill P. Radiation induced DNA DSBs: contribution from stalled replication forks? DNA Repair. 2010;9:907–913. doi:10.1016/j.dnarep.2010.06.002
DOI: https://doi.org/10.2478/gsr-2024-0012 | Journal eISSN: 2332-7774
Language: English
Page range: 159 - 176
Published on: Nov 23, 2024
Published by: American Society for Gravitational and Space Research
In partnership with: Paradigm Publishing Services
Publication frequency: 2 times per year
Related subjects:
© 2024 Amrita Singh, Sergio R. Santa Maria, Diana M. Gentry, Lauren C. Liddell, Matthew P. Lera, Jessica A. Lee, published by American Society for Gravitational and Space Research
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.