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| DC Field | Value | Language |
|---|---|---|
| dc.contributor.advisor | CUYPERS, Ann | - |
| dc.contributor.advisor | HOREMANS, Nele | - |
| dc.contributor.author | KARIUKI, Jackline | - |
| dc.date.accessioned | 2019-10-17T09:03:04Z | - |
| dc.date.available | 2019-10-17T09:03:04Z | - |
| dc.date.issued | 2019 | - |
| dc.identifier.uri | http://hdl.handle.net/1942/29773 | - |
| dc.description.abstract | Ionizing radiation (IR) is always present in the environment as it is constantly being emanated from natural sources (such as cosmic rays and naturally occurring radionuclides embedded within the earth’s crust) and man-made sources (such as controlled releases from the medical industry and accidental releases from nuclear power plants). The recent anthropogenic-induced increase of radioactive elements in nature has augmented the risk of exposure of living organisms. Since plants have a sessile lifestyle, they cannot escape the potentially harmful conditions. Previous studies have demonstrated that IR can affect plant growth. At the cellular level, excess production of reactive oxygen species (ROS) can be triggered in plants, which if not regulated results in the induction of oxidative stress. Excess ROS can, if not regulated properly, cause damage to important biomolecules such as DNA, proteins and membrane lipids. Nevertheless, plants are equipped with robust antioxidative defence and repair mechanisms that are activated following suitable alterations in gene expression by molecules such as the small non-coding RNAs including microRNAs (miRNAs). Despite knowledge on the responses elicited in plants shortly after exposure to IR, there is, so far, very little information on the effects elicited when plants are allowed to recover from irradiation. Such recovery studies are vital as they may help to not only determine the long-term consequences of radiation exposure in plants, but also, provide more insight into the mechanisms underpinning plant responses to IR. To this end, the first part of this study set out to investigate both irradiation and recovery responses in 1-week old Arabidopsis seedlings that were exposed to different gamma dose rates (27.2 mGy/h, 48.8 mGy/h and 103.5 mGy/h) for 2 weeks and allowed to recover for 4 days (Chapter 3). Two endpoints: rosette biomass and antioxidative capacity, were compared at the plant and metabolic levels, respectively. At the molecular level, a high-throughput mRNA sequencing analysis was carried out to gain more insight into the mechanisms triggered. From this study, it was established that Arabidopsis plants are able to recover from gamma radiation in a dose rate-dependent manner and that these plants employ different strategies at the molecular level to ensure survival both during irradiation and during recovery thereafter. Furthermore, the observed induction of early flowering during recovery in irradiated compared to control plants coupled with the differential expression of some senescence and flowering genes at the molecular level confirmed the hypothesis that early aging is induced in plants following gamma irradiation, which in the long run has an impact on development. This study also aimed at comparing the differences in radiosensitivity between Arabidopsis and the economically important rice (Oryza sativa) since the former was considered to be less sensitive to radiation compared to the latter. Therefore, responses elicited in rice plants following irradiation and recovery were also investigated by exposing 1-week old seedlings to different gamma dose rates that were comparable to those used for Arabidopsis. Rice plants were irradiated for 2 weeks and allowed to recover for another 2 weeks and sampling was done according to leaf age (Chapter 4). Leaf 4 was sampled after irradiation because it emerged during the treatment period and as a follow up, the same leaf 4 was sampled after the recovery period. In addition, leaf 7 was sampled after the recovery period as it developed during this time, thus, unlike leaf 4, the elongating/maturing cells of leaf 7 were not directly exposed to gamma radiation. The results obtained following the analysis of various endpoints in leaf 4 such as plant biomass, antioxidative potential, lignin content and the expression profiles of some important rice genes (antioxidative stress gene transcripts and DNA damage repair genes) revealed that rice plants are also able to recover from gamma radiation through the establishment of a new homeostasis. On the other hand, in leaf 7 of recovering plants, there was a radiation-induced signature even though the maturing cells of this leaf were not directly irradiated. As a result, it was proposed that a signalling mechanism comes into play during plant recovery that enables the establishment of a systemic acquired acclimation, which may serve to protect the plant in the event of future exposure to IR. The mRNA sequencing analysis conducted on Arabidopsis (Chapter 3) revealed that numerous genes were differentially expressed following irradiation and recovery. Gene expression changes have been shown to be coordinated by small non-coding RNA molecules referred to as microRNAs. So far, very few studies have identified gamma radiation-responsive miRNAs and furthermore, no efforts have been made to determine the miRNA expression profile in plants that have been allowed to recover from irradiation. Therefore, in the final part of this study, gamma radiation-responsive microRNAs in rice plants and the regulatory roles they play in mediating the responses elicited in irradiated and recovering plants, were investigated (Chapter 5). A small RNA sequencing analysis was carried out on libraries prepared from leaf 5 of irradiated and leaf 5 (follow-up) and 7 (maturing cells not directly irradiated) of recovering rice plants that had been exposed to two different gamma dose rates (48 and 107 mGy/h) for 2 weeks and allowed to recover for 2 weeks. Based on the differential expression of several rice miRNAs, this study showed for the first time that miRNAs play an essential role in regulating gene expression in both irradiated and recovering plants. In conclusion, the results of this PhD study demonstrate that both Arabidopsis and rice plants are able to recover from radiation exposure through overall molecular influence of growth, development and the physiological status. We also demonstrate that, in contrast to a statement in literature, rice plants, under the current experimental conditions used, are not more radiosensitive compared to Arabidopsis. Taken together, the information gained from this study will contribute towards a more comprehensive mechanistic understanding of IR-induced effects in living systems, which will allow for the strengthening of current legislation that has been formulated towards radiation protection of the environment. | - |
| dc.description.sponsorship | SCK•CEN (Belgian Nuclear Research Centre) | - |
| dc.language.iso | en | - |
| dc.subject.other | Ionizing radiation; Responses; Recovery; Arabidopsis; Rice | - |
| dc.title | Understanding the biological responses to ionizing radiation in plants after exposure and recovery: molecular profiling of Arabidopsis thaliana and Oryza sativa | - |
| dc.type | Theses and Dissertations | - |
| local.format.pages | 224 | - |
| local.bibliographicCitation.jcat | T1 | - |
| dc.relation.references | Abdel-Ghany S.E., Pilon M. (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J Biol Chem., 283(23): 15932–45. Abramov V.I., Fedorenko O.M., Shevchenko V.A. (1992) Genetic consequences of radioactive contamination for populations of Arabidopsis. Sci. Total Environ., 112: 19-28. Achard P., Herr A., Baulcombe D.C., Harberd N.P. (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development, 131: 3357-3365. Alonso-peral M.M., Li J., Li Y., Allen R.S., Schnippenkoetter W., et al. (2010) The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol., 154: 757–771. Alscher R.G., Erturk N., Heath L.S. (2002) Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. Journal of Experimental Botany, 53: 1331-1341. Amiro B.D., 1994. Response of Boreal forest tree canopy cover to chronic gamma irradiation. J. Environ. Radioact., 24:181-197. Andersson P., Beaugelin-Seiller K., Beresford N.A., Copplestone D., Della Vedova C., Garnier-Laplace J., Howard B.J., Howe P., Oughton D.H., Wells C. and Whitehouse P. (2008) Numerical benchmarks for protecting biota from radiation in the environment: proposed levels, underlying reasoning and recommendations. PROTECT Deliverable 5. EC contract number: 036425 (FI6R). Apel K., Hirt H. (2004). Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annual Review of Plant Biology, 55: 373-399. Arena C., De Micco V., De Maio A. (2014a). Growth alteration and leaf biochemical responses in Phaseolus vulgaris exposed to different doses of ionising radiation, Plant Biol., 16: 194–202. Arena, C., De Micco, V., Macaeva, E., Quintens, R. (2014b). Space radiation effects on plant and mammalian cells. Acta Astronaut. 104,:419–431. Arora A., Sairam R.K., Srivastava G.C. (2002) Oxidative stress and antioxidative system in plants. Current Science, 82: 1227– 1238. Asai K., Satoh N., Sasaki H., Satoh H., Nagato Y. (2002) A rice heterochronic mutant, mori1, is defective in the juvenile-adult phase change. Development, 129(1): 265-273. ASTDR. (2013) Toxicological profile for Uranium. In. Atlanta: U.S. Department of Health and Human Services. Agency for Public Substances and Disease Registry. Aukerman M.J., Sakai H. (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell, 15: 2730-2741. Avramova V., Abdelgawad H., Zhang Z., Fotschki B., Casadevall R., Vergauwen L., Knapen D.,Taleisnik E., Guisez Y., Asard H., Beemster G.T.S. (2015) Drought induces distinct growth response, protection, and recovery mechanisms in the maize leaf growth zone. Plant Physiol., 169: 1382–1396. Axtell M.J., Westholm J.O., Lai E.C. (2011) Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol., 12: 221. Bakhshi B., Fard E.M., Nikpay N., Ebrahimi M.A., Bihamta M.R., Mardi M., Salekdeh G.H. (2016). MicroRNA signatures of drought signaling in rice root. PLoS ONE, 11:e0156814. Baranauskė S., Mickutė M., Plotnikova A., Finke A., Venclovas Č., Klimašauskas S., Vilkaitis G. (2015). Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Res., 43: 2802–2812. Bar-Even A., Noor E., Lewi, N. E., Milo R. (2010) Design and analysis of synthetic carbon fixation pathways. Proc. Natl Acad. Sci. USA, 107: 8889–8894. Bariola P.A., Howard C.J., Taylor C.B., Verburg M.T., Jaglan V D., Green P.J. (1994) The Arabidopsis ribonuclease gene RNS1 is tightly controlled in response to phosphate limitation. Plant J., 6: 673–685. Barrera-Figueroa B.E., Gao L., Wu Z., Zhou X., Zhu J., Jin H., Liu R., Zhu J.K. (2012) High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol., 12:132. Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116: 281–297. Bartel, D.P. (2009) MicroRNAs: Target recognition and regulatory functions. Cell, 136: 215-233. Baumstark-Khan C., Facius R. (2001) Life under conditions of ionizing radiation. In Astrobiology: The Quest for the Conditions of Life, edited by G. Horneck and C. Baumstark-Khan, Springer, Berlin: 260–283. Bechtold U., Field B. (2018). Molecular mechanisms controlling plant growth during abiotic stress. J. Exp. Bot., 69 2753–2758. Benzie I.F. and Strain J.J. (1996) The ferric reducing ability of plasma (FRAP) as a measure of "antioxidant power": the FRAP assay. Anal. Biochem., 239 (1): 70-76. Beresford N.A., Copplestone D. (2011) Effects of ionising radiation on wildlife: what knowledge have we gained between the Chernobyl and Fukushima accidents? Integr. Environ. Assess. Manag., 7 (3): 371-373. Bhatt K, Sarma A, Thaker V. (2008) Effect of 7Li radiation on endogenous hormonal level on developing cotton fiber .Indian Journal of Experimental Biology, 46: 673-676. Biermans G., Horemans N., Vanhoudt N., Vandenhove H., Saenen E., Van Hees M., Wannijn J., Vangronsveld J. and Cuypers A. (2015) Arabidopsis thaliana seedlings show an age-dependent response on growth and DNA repair after exposure to chronic gamma-radiation. Environmental and Experimental Botany, 109: 122-30. Bitarishvili S.V., Volkova P., Geras'kin S. (2018) γ-Irradiation of barley seeds and its effect on the phytohormonal status of seedlings. Russ. J. Plant Physiol., 65: 446-454. Bleuyard J.Y., Gallego M.E., White C.I. (2006) Recent advances in understanding of the DNA double-strand break repair machinery of plants. DNA Repair (Amst), 5:1–12. Blokhina O., Virolainen E., Fagerstedt K.V. (2003) Antioxidants Oxidative damage and Oxygen deprivation stress: A review, Annal. Bot., 91: 179 - 194. Bolle C. (2004) The role of GRAS proteins in plant signal transduction and development. Planta, 218: 683–692. Borner R., Kampmann G., Apel K., Melzer S. (2000) The FPF gene family and flowering time control in Arabidopsis. (In) Proceedings of the 11th international conference on Arabidopsis research, abstract#308, Madison. Bowler C., Van Camp W., Van Montagu M., Inzé D. (1994) Superoxide dismutase in plants. Critical Reviews in Plant Sciences, 13: 199-218. Bowler C., Van Montagu M., Inzé D. (1992) Superoxide dismutase and stress tolerance. Annual Review of Plant Physiology and Plant Molecular Biology, 43: 83-116. Bray C., West C. (2005) DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity. New Phytologist, 168: 511-528. Brit, A.B. (1999). Molecular genetics of DNA repair in higher plants. Trends Plant Sci., 4(1), 20-25. Britt A.B. (1996). DNA damage and repair in plants. Annual Review of Plant Physiology and Plant Molecular Biology, 47, 75-100. Brodersen P., Sakvarelidze-Achard L., Bruun-Rasmussen M., Dunoyer,P., Yamamoto Y.Y., Sieburth L., Voinnet O. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320: 1185–1190. Brown J.E., Alfonso B., Avila,R., Beresford N.A., Copplestone D., Prohl G. and Ulanovsky, A. (2008) The ERICA tool. J. Environ. Radioact., 99 (9): 1371-1383. Buchanan-Wollaston V., Earl S., Harrison E., Mathas E., Navabpour S., Page T., Pink D. (2003) The molecular analysis of leaf senescence - a genomics approach. Plant Biotechnol J., 1: 3–22. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem, 55(4): 611-622. Cabane, M., Afif, D., Hawkins, S. (2012) Lignins and Abiotic Stresses. In L. Jouann and C. Lapierre (Eds.), Lignins: Biosynthesis, Biodegradation and Bioengineering, 61: 219-262. Caplin N., Willey N. (2018) Ionizing radiation, higher plants, and radioprotection: from acute high doses to chronic low doses. Front Plant Sci., 9: 847. Casati P. (2013) Analysis of UV-B regulated miRNAs and their targets in maize leaves. Plant Signal. Behav., 8: 4161, 26758. Chae H.S., Kieber J.J. (2005) Eto brute? Role of ACS turnover in regulating ethylene biosynthesis. Trend Plant Sci., 10: 291-296. Cheah B.H., Nadarajah K., Divate M.D., Wickneswari R. (2015). Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage. BMC Genomics, 16:692. Cheema A.A., Atta B.M. (2003) Radiosensitivity studies in Basmati rice. Pakistan Journal of Botany, 35(2): 197-207. Chellappan P., Xia J., Zhou X., Gao S., Zhang X., Coutino G., Vazquez F., Zhang W., Jin H. (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res, 38(20): 6883–6894. Chen H., Kobayashi K., Miyao A., Hirochika H., Yamaoka N., Nishiguchi M. (2013) Both OsRecQ1 and OsRDR1 are required for the production of small RNA in response to DNA-damage in rice. PLoS One, 8(1), e55252. Chen W., et al. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant cell, 14: 559-574. Chen X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303:2022-2025. Chiruvella K.K., Liang Z., Wilson T.E. (2013) Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol., 5:a012757. Chung B.C., Lee S.Y., Oh S.A., Rhew T.H., Nam H.G., Lee C.H. ( 1997) The promoter activity of sen1, a senescence associated gene of Arabidopsis is repressed by sugars. J. Plant Physiol., 151: 339– 345. Ciccia A., Elledge S.J. (2010) The DNA damage response: Making it safe to play with knives. Mol. Cell, 40:179–204. Claeys H., Van Landeghem S., Dubois M., Maleux K., Inze D. (2014) What is stress? Dose-response effects in commonly used in vitro stress assays. Plant Physiol. 165: 519–527. Cock J., Yoshida S., Forno D.A. (1976) Laboratory manual for physiological studies of rice. Int. Rice Res. Inst. Cojocaru, A.F., Revin, A.F. (2010) Investigation of mechanism of γ-irradiation action on the biosynthesis of indole derivatives and their role in energy formation in plant seedlings, Sovrem. Probl. Nauki Obraz., 4: 8–18. Coles J.P., Phillips A.L., Croker S.J., Garcia-Lepe R., Lewis M.J., Hedden P. (1999) Modification of gibberellin production and plant development in Arabidopsis by sense and antisense expression of gibberellin 20-oxidase genes. Plant J., 17: 547-556. Combier J.P., Frugier F., de Billy F., Boualem A., El-Yahyaoui F., Moreau S., Vernie T., Ott T., Gamas P., Crespi M., et al., (2006) MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes Dev., 20: 3084–3088. Cominelli, E., Tonelli, C. (2009) A new role for plant R2R3-MYB transcription factors in cell cycle regulation. Cell Res., 19: 1231–1232. Cosio, C., Dunand, C. (2009) Specific functions of individual class III peroxidase genes. Journal of Experimental Botany, 60: 391– 408. Cowart J.B., Burnett W.C. (1994) The distribution of uranium and thorium decay-series radionuclides in the environment – a review. Journal of Environmental Quality, 23: 651- 662. Crisp P.A., Ganguly D., Eichten S.R., Borevitz J.O., Pogson B.J. (2016) Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics. Science Advances, 2(2), e1501340. Crisp P.A., Ganguly D.R., Smith A.B., Murray K.D., Estavillo G.M., Searle I., et al. (2017). Rapid recovery gene down-regulation during excess-light stress and recovery in Arabidopsis. Plant Cell 29: 1836–1863. Cui L.G., Shan J.X., Shi M., Gao J.P., Lin H.X. (2014) The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J., 80: 1108–1117. Culligan, K.M., Robertson, C.E., Foreman, J., Doerner, P., Britt A.B. (2006) ATR and ATM play both distinct and additive roles in response to ionizing radiation. Plant J., l48: 947–961. Curaba, J., Singh, M. B., and Bhalla, P. L. (2014) miRNAs in the crosstalk between phytohormone signalling pathways. J. Exp. Bot., 65, 1425–1438. Dai X., Zhuang Z. and Zhao P.X. (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res., 46: W49-W54. Daly K., Thompson K.H. (1975) Quantitative dose response of growth and development in Arabidopsis thaliana exposed to chronic gamma radiation. Int. J. Radiat. Biol., 28:61-66. Dartnell L.R. (2011) Ionizing radiation and life. Astrobiology, 11: 551-582. Das Gupta M., Nath U. (2015) Divergence in patterns of leaf growth polarity is associated with the expression divergence of miR396. Plant Cell, 27: 2785–2799. Das K., Roychoudhury A. (2014) Reactive oxygen species (ROS) and response of antioxidants as ROS-scavengers during environmental stress in plants. Front. Environ., Sci., 2: 53. Dat J., Vandenabeele S.., Vranova E., Van Montagu M., Inze D., Van Breusegem F. (2000) Dual action of the active oxygen species during plant stress responses. Cellular and Molecular Life Sciences, 57: 779-795. Dave A., Graham I.A. (2012) Oxylipin signalling: a distinct role for the jasmonic acid precursor cis-(+)-12-oxo-phytodienoic acid (cis-OPDA). Front Plant Sci., 3: 42. Davies C. R. (1968) Effects of gamma irradiation on growth and yield of agricultural crops--I. Spring sown wheat. Radiat. Bot., 8: 17-30. De Veylder L., Beeckman T., Beemster G.T.S., Krols L., Terras F., Landrieu I., Van Der Schueren E., Maes S., Naudts M., Inzé D. (2001). Functional analysis of cyclin-dependent kinase inhibitors of Arabidopsis. Plant Cell, 13: 1653–1667. Ding Y.F., Chen Z., Zhu C. (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot., 62 (10): 3563-3573. Dmitrieva, S.A. (1996) The adaptation of natural plant populations to chronic irradiation due to the accident at the Chernobyl Atomic Electric Power Station. Tsitol Genet., 30(4): 3-8. Domenichini S., Raynaud C., Ni D.A., Henry Y. and Bergounioux C. (2006) Atmnd1-δ1 is sensitive to γ-irradiation and defective in meiotic DNA repair. DNA Repair (Amst.), 5: 455–464. Doucet-Chabeaud G., Godon C., Brutesco C. Murcia G. de., Kazmaier M. (2001) Ionising radiation induces the expression of PARP-1 andPARP-2 genes in Arabidopsis. Mol Gen Genomics, 265: 954. Eisler, R. (1994) Radiation hazards to fish, wildlife, and invertebrates: a synoptic review. Biological Report 26. National Biological Service, Washington, D.C. Endo, S., Kajimoto, T., Shizuma, K. (2013)Paddy-field contamination with 134Cs and 137Cs due to Fukushima Dai-ichi Nuclear Power Plant accident and soil-to-rice transfer coefficients. J. Environ. Radioact., 116, 59–64. Esnault M. A., Legue F., Chena C. (2010) Ionizing radiation: advances in plant response. Environ. Exp. Bot., 68: 231–237. Fan T., Li X., Yang W., Xia K., Ouyang J., Zhang M. (2015) Rice miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors. PLoS ONE 10(5): e0125833. Fang Y, Xie K, Xiong L. (2014) Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J Exp Bot., 65: 2119-2135. Floyd S.K., Bowman J.L. (2004) Ancient microRNA target sequences in plants. Nature, 428: 485-486. Fortunati, A., Tassone, P., Damasso, M., Migliaccio, F. (2010) Neutron irradiation affects the expression of genes involved in the response to auxin, senescence and oxidative stress in Arabidopsis, Plant Signal. Behav., 5: 959–967. Fouracre, J.P., Poethig, R.S. (2016) The role of small RNAs in vegetative shoot development. Curr. Opin. Plant Biol. 29: 64–72. Foyer C.H. and Noctor G. (2005) Redox homeostasis and antioxidant signaling: a metabolic interface between stress perception and physiological responses. Plant Cell 17, 18661875. Foyer C.H., Descouvrières P., Kunert K.J. (1994) Protection against oxygen radicals: an important defence mechanism studied in transgenic plants. Plant, Cell and Environment 17: 507-523. Foyer C.H., Lopez Delgado H., Dat J.F., Scott I.M. (1997) Hydrogen peroxide and glutathione associated mechanisms of acclimatory stress tolerance and signalling. Physiologia Plantarum, 100(2): 241-254. Foyer C.H., Noctor G. (2011) Ascorbate and glutathione: The heart of the redox hub. Plant Physiol., 155: 2–18. Foyer C.H., Noctor G. (2011) Ascorbate and glutathione: The heart of the redox hub. Plant Physiol., 155: 2–18. Frank H.A., Brudvig G.W. (2004) Redox functions of carotenoids in photosynthesis. Biochemistry, 43(27): 8607-8615. Friedlander M.R., Mackowiak S.D., Li N., Chen W., Rajewsky N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40 (1): 37-52. Friesner J., Britt A.B. (2003) Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration. Plant J., 34: 427-440. Fujii H., Chiou T.J., Lin S.I., Aung K., Zhu J.K. (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr. Biol., 15: 2038-2043. Fujiki Y., Yoshikawa Y., Sato T., Inada N., Ito M., Nishida I., Watanabe A. ( 2001) Dark‐inducible genes from Arabidopsis thaliana are associated with leaf senescence and repressed by sugars. Physiologia Plantarum, 111: 345– 352. Furukawa T., Imamura T., Kitamoto H.K., Shimada H. (2008) Rice exonuclease-1 homologue, OsEXO1, that interacts with DNA polymerase lambda and RPA subunit proteins, is involved in cell proliferation. Plant Mol Biol., 66(5): 519-531. Gadjev I., Vanderauwera S., Gechev T.S., Laloi C., Minkov I.N., Shulaev V., Apel K., Inzé D., Mittler R., Van Breusegem F. (2006) Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol., 141: 436–445. Gallego M.E., Bleuyard J.Y., Daoudal‐Cotterell S., Jallut N., White C.I. (2003) Ku80 plays a role in non‐homologous recombination but is not required for T‐DNA integration in Arabidopsis. Plant Journal, 35: 557–565. Gao Q.M., Zhu S., Kachroo P., Kachroo A. (2015) Signal regulators of systemic acquired resistance. Frontiers in plant science, 6: 228-228. Garg N., Manchanda G. (2009) ROS generation in plants: boon or bane? Plant Biosystems, 143: 81-96. Garnier-Laplace J., Geras'kin S., Della-Vedova C., Beaugelin-Seiller K., Hinton T.G., Real A., Oudalova A. (2013) Are radiosensitivity data derived from natural field conditions consistent with data from controlled exposures? A case study of Chernobyl wildlife chronically exposed to low dose rates. Journal of Env. Rad., 121: 12-21. Garnier-Laplace J., Gilbin R. (2006) Derivation of predicted no effect dose rates for ecosystems (and their sub-organizational levels) exposed to radioactive substances. Deliverable D5. European Commission, 6th Framework, Contract No. FI6RCT-2003-508847. Georgieva M., Rashydov N.M., Hajduch M. (2017) DNA damage, repair monitoring and epigenetic DNA methylation changes in seedlings of Chernobyl soybeans. DNA Repair, 50, pp. 14-21. Gicquel M., Taconnat L., Renou J.P., Esnault M.A., Hurtado F.C. (2012) Kinetic transcriptomic approach revealed metabolic pathways and genotoxic-related changes implied in the Arabidopsis response to ionizing radiations. Plant Sci., 195: 106-119. Gielen H., Remans T., Vangronsveld J., Cuypers A. (2016) Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7. BMC Plant Biology, 16: 145. Gigolashvili T., Kopriva S. (2014) Transporters in plant sulphur metabolism. Front. Plant Sci., 5:422. Gill S.S., Tuteja N. (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol. Biochem., 48: 909–930. Gimenez E., Manzano-Agugliaro F. (2017) DNA damage repair system in plants: a worldwide research update. Genes (Basel) 8: 299. Goh E.J., Kim J.B., Kim W.J., Ha B.K., Kim S.H., Kang S.Y., Seo Y.W., Kim D.S. (2014) Physiological changes and anti-oxidative responses of Arabidopsis plants after acute and chronic gamma irradiation. Radiat. Environ. Biophys. 53: 677–693. Goldberg R., Catesson A.-M., Czaninski Y. (1983) Some Properties of syringaldazine oxidase, a peroxidase specifically involved in the lignification processes. Zeitschrift für Pflanzenphysiologie, 110(3): 267-279. Großkinsky D. K., van der Graaff E., Roitsch T. (2016) Regulation of abiotic and biotic stress responses by plant hormones. Plant Pathogen Resistance Biotechnology, ed. D. B. Collinge (New York, NY: Wiley and Sons): 131–134. Guadagno, C.R., Ewers, B.E., Weinig C. (2018). Circadian Rhythms and Redox State in Plants: Till Stress Do Us Part. Frontiers in plant science, 9: 247-247. Gunckel J.E. (1957) The effect of ionizing radiation on plants morphological effects. Q. Rev. Biol. 32(1): 46-5. Guo H.S., Xie Q., Fei J.F., Chua N.H. (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell, 17: 1376-1386. Ha M., Kim V. N. (2014) Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol., 15: 509–524. Halliwell B. (2006) Reactive species and antioxidants. Redox biology is a fundamental theme of aerobic life. Plant Physiology, 141: 312-322. Harding S.S, Johnson S.D., Taylor D.R., Dixon C.A., Turay M.Y. (2012) Effect of gamma rays on seed germination, seedling height, survival percentage and tiller production in some rice varieties cultivated in Sierra Leone. American Journal of Experimental Agriculture, 2(2): 247-255. Hayashi G., Shibato J., Imanaka T., Cho K., Kubo A., Kikuchi S., Satoh K., Kimura S., Ozawa S., Fukutani S., Endo S., Ichikawa K., Agrawal G.K., Shioda S., Fukumoto M., Rakwal, R. (2014) Unraveling low-level gamma radiation-responsive changes in expression of early and late genes in leaves of rice seedlings at Iitate Village, Fukushima. J Hered., 105(5): 723-738. He D.L., Wang Q., Wang K., Yang P.F. (2015) Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination. PLoS One, 10(12): e0145424. Health Physics Society [HPS] (2015). Background Radiation. Henderson I.R., Zhang X., Lu C., Johnson L., Meyers B.C., Green P.J., Jacobsen S.E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet., 38: 721–5. Hewezi T., Maier T.R., Nettleton D., Baum T.J. ( 2012) The Arabidopsis microRNA396‐GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiol., 159: 321– 335. Hiraga S., Sasaki K., Ito H., Ohashi Y., Matsui H. (2001) A large family of class III plant peroxidases. Plant Cell Physiol., 42: 462–468. Hofacker I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31: 3429-3431. Hong M.J., Kim D.Y., Ahn J.W., Kang S.Y., Seo Y.W., Kim, J.B. (2018). Comparison of radiosensitivity response to acute and chronic gamma irradiation in colored wheat. Genet Mol Biol, 41(3): 611-623. Hong M.J., Kim J.B., Yoon Y.H., Kim S.H., Ahn J.W., Jeong I.Y., Kim D.S., (2014) The effects of chronic gamma irradiation on oxidative stress response and the expression of anthocyanin biosynthesis-related genes in wheat (Triticum aestivum). Int. J. Radiat. Biol. 90 (12): 1218–1228. Hou X., Zhou J., Liu C., Liu L., Shen L., Yu H. (2014). Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat. Commun., 5: 4601. Hu W., Wang T., Xu J. and Li H. (2014) MicroRNA mediates DNA methylation of target genes. Biochem Biophys Res Commun., 444(4): 676–681. Huang S.Q., Peng J., Qiu C.X., Yang Z.M. (2009) Heavy metal-regulated new microRNAs from rice. J Inorg Biochem., 103 (2): 282-28. Huefner N.D., Yoshiyama K., Friesner J.D., Conklin P.A., Britt A.B. (2014) Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana. Frontiers in Plant Science, 5: 7. Huot B., Yao J., Montgomery B.L., He S.Y. (2014) Growth-defense tradeoffs in plants: A balancing act to optimize fitness. Mol. Plant 7, 1267–1287. Hwang S.G, Kim D.S., Kim J.B., Hwang J.E., Park H.M., Kim J.H., Jang C.S. (2016) Transcriptome analysis of reproductive-stage Arabidopsis plants exposed gamma-ray irradiation at various doses. International Journal of Radiation Biology, 92:8, 451-465. Hwang, S.G., Kim, D.S., Hwang, J.E., Han, A.R., Jang, C.S. (2014) Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis. Gene, 541(2), 82-91. IAEA. (1992) Effects of Ionizing Radiation on Plants and Animals at Levels Implied by Current Radiation Protection Standards. Technical Reports Series No. 332. International Atomic Energy Agency (IAEA), Vienna. IAEA. (2002) Ethical Considerations in Protecting the Environment From the Effects of Ionizing Radiation: A Report for Discussion. IAEA-TECDOC-1270. International Atomic Energy Agency (IAEA), Vienna. IAEA. (2005) Draft Plan of Activities on the Radiation Protection of the Environment. GOV/2005/49 (24 August. International Atomic Energy Agency (IAEA), Vienna. IAEA. (2006) Environmental consequences of the Chernobyl accident and their remediation: twenty years of experience. Report of the Chernobyl Forum Expert Group ‘Environment. International Atomic Energy Agency (IAEA), Vienna. IAEA. (2018) Prospective Radiological Environmental Impact Assessment for Facilities and Activities. IAEA Safety Standards Series No. GSG-10. International Atomic Energy Agency (IAEA), Vienna. ICRP. (2007) The 2007 Recommendations of the International Commission on Radiological Protection. ICRP Publication 103. Ann. ICRP 37 (2-4). ICRP. (2008) Environmental protection - the concept and use of reference animals and plants. ICRP publication 108. Ann. ICRP, 38 (4–6). ICRP. (2014) Protection of the environment under different exposure situations. ICRP publication 124. Ann. ICRP, 43 (1). ICRP. (2017) Dose coefficients for nonhuman biota environmentally exposed to radiation. ICRP Publication 136. Ann. ICRP 46(2). Iiyama K., Wallis A.F.A. (1990) Determination of lignin in herbaceous plants by an improved acetyl bromide procedure. Journal of the Science of Food and Agriculture, 51(2): 145-161. Im J., Kim W.J., Kim S.H., Ha B.K. (2017) Effects of proton beam irradiation on seed germination and growth of soybean (Glycine max L. Merr.). Journal of the Korean Physical Society, 71(11): 752-757. Imaizumi T., Schultz T.F., Harmon F.G., Ho L.A., Kay S.A. (2005) FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science, 309: 293-297. Iqbal N., Khan N. A., Ferrante A., Trivellini A., Francini A., Khan M.I.R. (2017) Ethylene role in plant growth, development and senescence: interaction with other phytohormones. Front. Plant Sci., 8:475. Irfaq, M., Nawab, K. (2001) Effect of gamma irradiation on some morphological characteristics of three wheat ( Triticum aestivum L.) Cultivars. International Journal Biology and Science 1(10): 935-937. Itoh J.I., Nonomura K.I., Ikeda K., Yamaki S., Inukai Y., Yamagishi H., Kitano H., Nagato Y. (2005) Rice Plant Development: from Zygote to Spikelet. Plant and Cell Physiology, 46(1), 23-47. Ivanov B.N., Khorobrykh S. (2003) Participation of photosynthetic electron transport in production and scavenging of reactive oxygen species. Antioxidants and Redox Signaling, 5 (1): 43–53. Ivashuta S., Banks I.R., Wiggins B.E., Zhang Y., Ziegler T.E., James K., Heck G.R. (2011) Regulation of gene expression in plants through miRNA inactivation. PLoS One, 6 (6): e21330. Iwakawa H.O., Tomari Y. (2015) The functions of microRNAs: mRNA decay and translational repression. Trends Cell Biol., 25: 651–665. Jan S., Parween T., Siddiqi T.O., Mahmooduzzafar X. (2012) Effect of gamma radiation on morphological, biochemical and physiological aspects of plants and plant products. Environ Rev., 20: 17−39. Jia X., Ren L., Chen Q.J., Li R.,Tang G. (2009) UV-B-responsive microRNAs in Populus tremula. J Plant Physiol., 166 (18): 2046-2057. Jing H.C., Schippers J.H., Hille J., Dijkwel P.P. (2005) Ethylene-induced leaf senescence depends on age-related changes and OLD genes in Arabidopsis. J. Exp. Bot., 56:2915–23. John I., Drake R., Farrell A., Cooper W., Lee P., Horton P., Grierson D. (1995) Delayed leaf senescence in ethylene‐deficient ACC‐oxidase antisense tomato plants: molecular and physiological analysis. The Plant Journal 7: 483–490. Jones-Rhoades M.W., Bartel D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14: 787–799. Jones-Rhoades M.W., Bartel D.P., Bartel B. (2006) MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol., 57: 19-53. Jossen R., Bermejo R. (2013) The DNA damage checkpoint response to replication stress: a Game of Forks. Front. Genet. 4:26. Jung I.J., Hwang J.E., Han S.M., Kim D.S., Ahn J.W., Choi H.I., Kwon S.J., Kang S.Y., Kim J.B. (2017). Molecular dissection of the response of the rice Systemic Acquired Resistance Deficient 1 (SARD1) gene to different types of ionizing radiation. Int J Radiat Biol, 93(7): 717-725. Kanegae H., Miyoshi K., Hirose T., Tsuchimoto S., Mori M., Nagato Y., Takano M. (2005) Expressions of rice sucrose non-fermenting-1 related protein kinase 1 genes are differently regulated during the caryopsis development. Plant Physiol Biochem., 43: 669–679. Karuppanapandian T., Moon J.C., Kim C., Manoharan K., Kim W. (2011) Reactive oxygen species in plants: Their generation, signal transduction, and scavenging mechanisms. Aust. J. Crop Sci., 5:709–725. Katiyar-Agarwal S., Jin H. (2010) Role of small RNAs in host-microbe interactions. Annu. Rev. Phytopathol. 48: 225–246. Kaup M.T., Froese C.D., Thompson J.E. (2002) A role for diacylglycerol acyltransferase during leaf senescence. Plant Physiol. 129: 1616–1626 Kawahara Y., de la Bastide M., Hamilton J.P., et al. (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, pp. 4. Kawashima C.G., Yoshimoto N., Maruyama-Nakashita A., Tsuchiya Y.N., Saito K., Takahashi H., Dalmay T. (2009) Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J., 57: 313–321. Kazan K., Rebecca Lyons R. (2016) The link between flowering time and stress tolerance, Journal of Experimental Botany, 67: 47–60. Khan M., Rozhon W., Poppenberger B. (2014) The role of hormones in the aging of plants: a mini-review. Gerontology 60: 49–55. Khan M.I., Fatma M., Per T.S., Anjum N.A., Khan N.A. (2015) Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants. Front Plant Sci., 6: 462. Khraiwesh B., Arif M.A., Seumel G.I., Ossowski S., Weigel D., Reski R., Frank W. (2010) Transcriptional control of gene expression by microRNAs. Cell, 140(1): 111–122. Khraiwesh B., Zhu J.K., Zhu J. (2011) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim. Biophys. Acta., 1819(2):137-48. Kim D.S., Kim J.B., Goh E.J., Kim W.J., Kim S.H., Seo Y.W., Jang C.S., Kang S.Y. (2011) Antioxidant response of Arabidopsis plants to gamma irradiation: Genome-wide expression profiling of the ROS scavenging and signal transduction pathways, Journal of Plant Physiology, 168: 1960-71. Kim D.S., Kim J.B., Goh E.J., Kim. W.J., Kim S.H., Seo Y.W., Jang C.S., Kang S.Y. (2011) Antioxidant response of Arabidopsis plants to gamma irradiation: genome-wide expression profiling of the ROS scavenging and signal transduction pathways. J. Plant Physiol., 168: 1960-1971. Kim D.Y., Hong M.J., Park C.S., Seo Y.W. (2015) The effects of chronic radiation of gamma ray on protein expression and oxidative stress in Brachypodium distachyon. Int J Radiat Biol., 91(5): 407-419. Kim H., Kim H.J., Vu Q.T., Jung S., McClung C.R., Hong S., Nam H.G. (2018) Circadian control of ORE1 by PRR9 positively regulates leaf senescence in Arabidopsis. PNAS, 115: 8448–8453. Kim J., Jung J.H., Reyes J.L., Kim Y-S., Kim S.Y., Chung K.S., Kim J.A., Lee M., Lee Y., Kim V.N. Chua N.H., Park C.M. (2005) microRNA cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J., 42: 84 -94. Kim J.B., Kim S.H., Ha B.K., Kang S.Y., Jang C.S., Seo Y.W., Kim D.S. (2014) Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana. Mol Biol Rep., 41:2229–2241. Kim J.H., Baek M.H., Chung B.Y., Wi S.G., Kim J.S. (2004) Alterations in the photosynthic pigments and antioxidant machineries of red pepper (Capsicum annuum L.) seedlings from gamma-irradiated seeds. J. Plant Biol., 47: 314-321 Kim J.H., Chung B.Y., Kim J.S., Wi S.G. (2005) Effects of in Planta gamma-irradiation on growth, photosynthesis and antioxidative capacity of red pepper (Capsicum annuum L.) plants. Journal of Plant Biology, 48(1): 47-56. Kim J.H., Chung B.Y., Kim J.S., Wi S.G. (2005) Effects of in planta gamma-irradiation on growth, photosynthesis, and antioxidative capacity of red pepper. J. Plant Biol., 48: 47-56. Kim J.H., Go Y.S., Kim J.K., Chung B.Y. (2016) Characterization of microRNAs and their target genes associated with transcriptomic changes in gamma-irradiated Arabidopsis. Genet Mol Res., 15 (3). Kim J.H., Moon Y.R., Lee M.H., Kim J.H., Wi S.G., Park B.J., Kim C.S., Chung B.Y. (2011) Photosynthetic capacity of Arabidopsis plants at the reproductive stage tolerates γ irradiation, J. Radiat. Res., 52: 441–449. Kim J.H., Moon Y.R., Kim J.S., Oh M.H., Lee J.W., Chung B.Y. (2007) Transcriptomic profile of Arabidopsis rosette leaves during the reproductive stage after exposure to ionizing radiation. Radiat. Res., 168: 267-280. Kim S., Yang J.Y., Xu J., Jang I.C., Prigge M.J., Chua N.H. (2008) Two Cap-Binding Proteins CBP20 and CBP80 are involved in Processing Primary MicroRNAs. Plant Cell Physiol., 49:1634–1644. Kim S.H., Song M., Lee K.J., Hwang S.G., Jang C.S., Kim J.B., Kim D.S. (2012) Genome-wide transcriptome profiling of ROS scavenging and signal transduction pathways in rice (Oryza sativa L.) in response to different types of ionizing radiation. Mol. Biol. Rep. 39 (12): 11231–11248. Kim V.N. (2004) MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol., 14: 156–159. Kim J.B., Kim S.H., Ha B.K., Kang S.Y., Jang C.S., Seo Y.W., Kim D.S. (2014) Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana. Mol Biol Rep., 41: 2229–2241 Kimura S., Shibato J., Agrawal G.K., Kim Y.K., Nahm B.H., Jwa N.S., Iwahashi H., Rakwal R. (2008) Microarray analysis of rice leaf response to radioactivity from contaminated Chernobyl soil. Rice Genet. Newsl., 24: 52–54. Kimura S., Tahira Y., Ishibashi T., Mori Y., Mori T., Hashimoto J., Sakaguchi K. (2004) DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells. Nucleic Acids Res., 32(9): 2760-2767. Kolvachuk I., Molinier J., Yao Y., Arkhipov A., Kovalchuk O. (2007) Transcriptome analysis reveals fundamental differences in plant response to acute and chronic exposure to ionizing radiation. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. J. Agric. Food Chem., 53: 1022-1030. Komaki S., Sugimoto K. (2012) Control of the plant cell cycle by developmental and environmental cues. Plant Cell Physiol. 53: 953–964. Kosová K., Vitamvas P., Urban M.O., Prasil I.T., Renaut J. (2018). Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome. Frontiers in Plant Science, 9:22. Kovalchuk I. (2018) Role of Epigenetics in Transgenerational Changes: Genome Stability in Response to Plant Stress. In: Baluska F., Gagliano M., Witzany G. (eds) Memory and Learning in Plants. Signaling and Communication in Plants. Springer, Cham Kovalchuk I., Abramov V., Pogribny I., Kovalchuk O. (2004) Molecular aspects of plant adaptation to life in the Chernobyl zone, Plant Physiology, 135: 357-63. Kovalchuk I., Kovalchuk O., Arkhipov A., Hohn B. (1998) Transgenic plants are sensitive bio-indicators of nuclear pollution caused by the Chernobyl accident. Nature Biotechnology, 16: 1054-59. Kovalchuk I., Molinier J., Yao Y., Arkhipov A., Kovalchuk O. (2007). Transcriptome analysis reveals fundamental differences in plant response to acute and chronic exposure to ionizing radiation. Mutat Res., 624(1-2): 101-113. Kovalchuk O., Arkhipov A., Barylyak I., Karachov I., Titov V., Hohn B., Kovalchuk I. (2000) Plants experiencing chronic internal exposure to ionizing radiation exhibit higher frequency of homologous recombination than acutely irradiated plants. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 449: 47-56. Kozak J., West C.E., White C., da Costa-Nunes J.A., Angelis K.J. (2009) Rapid repair of DNA double strand breaks in Arabidopsis thaliana is dependent on proteins involved in chromosome structure maintenance. DNA Repair (Amst), 8: 413–419. Kozlowska-Kalisz J. (1979) The influence of ionizing radiation on, biological activity of endogenous growth regulators in Orchids (Cymbidium) in tissue culture. Acta Horticulture. Symposium on Growth Regulators in Floriculture 91: 261-268. Kozubov, G.M., Taskaev, A.I. (2007) Characteristics of morphogenesis and growth processes of conifers in the Chernobyl nuclear accident zone. (in Russian) Radiats Biol. Radioecol., 47, 204–223. Krieger-Liszkay A. (2005) Singlet oxygen production in photosynthesis. J. Exp. Bot., 56: 337-346. Kurihara Y., Watanabe Y. (2004). Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A., 101: 12753–8. Lacombe S., Nagasaki H., Santi C., Duval D., Piegu B., Bangratz M., Breitler J.C., Guiderdoni E., Brugidou C., Hirsch J., Cao X., Brice C., Panaud O., Karlowski W.M., Sato Y., Echeverria M. (2008) Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice. BMC Plant Biol, 8: 123. Larkins B.A., Dilkes B.P., Dante R.A., Coelho C.M., Woo Y.M., Liu Y. (2001) Investigating the hows and whys of DNA endoreduplication. J. Exp. Bot. 52, 183–192. Larson R.A. (1988). The antioxidants of higher plants. Phytochemistry, 27(4): 969-978. Larsson C.M. (2008) An overview of the ERICA integrated approach to the assessment and management of environmental risks from ionizing contaminants. J. Environ. Radioact., 99: 1364-1370. Latif H.H., Abdalla M.A., Farag S.A. (2011) Radio-stimulation of phytohormons and bioactive components of coriander seedlings. Turkish J. Biochem., 36: 230-236. Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J.U., Rätsch G. and Weigel D. (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 105: 8795–8800. Laufs P., Peaucelle A., Morin H. Traas J. (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development, 131: 4311-4322. Lauter N., Kampani A., Carlson S., Goebel M. and Moose S.P. (2005) MicroRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. U.S.A., 102: 9412-9417. Le Gall H., Philippe F., Domon J.M., Gillet F., Pelloux J., Rayon C. (2015) Cell Wall Metabolism in Response to Abiotic Stress. Plants (Basel, Switzerland), 4(1): 112-166. Lee B.R., Kim K.Y., Jung W.J., Avice J.C., Ourry A., Kim T.H. (2007) Peroxidases and lignification in relation to the intensity of water-deficit stress in white clover (Trifolium repens L.). J Exp Bot, 58(6): 1271-1279. Lee M.B., Kim D.Y., Jeon W.B., Hong M.J., Lee Y.J., Bold O., Jang J.H., Kim Y.J., Kang S.Y., Kim D.S., Kim J.B., Chun J.B., Seo Y.W. (2013) Effect of gamma radiation on growth and lignin content in Brachypodium distachyon. Journal of Crop Science and Biotechnology, 16(2): 105-110. Lee R.C., Feinbaum R.L., Ambros V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75: 843-854. Leyva-Gonzalez M.A., Ibarra-Laclette E., Cruz-Ramirez A., Herrera-Estrella L. (2012) Functional and transcriptome analysis reveals an acclimatization strategy for abiotic stress tolerance mediated by Arabidopsis NF-YA family members. PLoS One.7(10): e48138. Li F., Vallabhaneni R., Yu J., Rocheford T., Wurtzel E.T. (2008) The maize phytoene synthase gene family: overlapping roles for carotenogenesis in endosperm, photomorphogenesis, and thermal stress tolerance. Plant Physiology, 147 (3): 1334-1346. Li F., Wang W., Zhao N., Xiao B., Cao P., Wu X., et al. (2015). Regulation of nicotine biosynthesis by an endogenous target mimicry of miRNA in tobacco. Plant Physiol., 169: 1062–1071. Li S., Liu L., Zhuang X., Yu Y., Liu X., Cui X., Ji L., Pan Z., Cao X., Mo B., Zhang F., Raikhel N., Jiang L., Chen X. (2013) MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell, 153: 562-574. Li W.X., Oono Y., Zhu J., He X.J., Wu J.M., Iida K., Lu X.Y., Cui X., Jin H., Zhu J.K. (2008) The Arabidopsis NF-YA5 transcription factor is regulated transcriptionally and post-transcriptionally to promote drought resistance. Plant Cell 20: 2238–2251. Li Y., Zhao S., Li J., Hu X., Wang H., Cao X., Xu Y., Zhao Z., Xiao Z., Yang N., Fan J., Huang F., Wang W. (2017) miR169 Negatively Regulates Rice Immunity against the Blast Fungus Magnaporthe oryzae. Frontiers in Plant Science, 8: 2. Li Y., Wang W., Wang T., Wouters M.A., Yin Y., Jiao Z., Ma L., Zhang F. (2018) Regulation through microRNAs in response to low-energy N+ ion irradiation in Oryza sativa. Radiation Research 191(2): 189-200. Lian S., Cho W.K., Kim S.M., Choi H., Kim, K.H. (2016) Time course small RNA profiling reveals rice miRNAs and their target genes in response to rice stripe virus infection. PLoS ONE, 11: e0162319. Liang G., He, H., Yu D. (2012) Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS ONE 7: e48951. Liang G., Yang F.X., Yu D.Q. (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. Plant J., 62: 1046–1057. Lim P.O., Kim H.J., Nam H.G. (2007) Leaf senescence. Annual Review of Plant Biology, 58: 115-136 Lim, P.O., Woo, H.R. and Nam, H.G. ( 2003) Molecular genetics of leaf senescence in Arabidopsis. Trends in Plant Science, 8: 272– 278. Liu G.T., Ma L., Duan W., Wang B.C., Li J.H., Xu H.G., Yan X.Q., Yan B.F., Li S.H., Wang, L.J. (2014) Differential proteomic analysis of grapevine leaves by iTRAQ reveals responses to heat stress and subsequent recovery. BMC Plant Biol, 14: 110. Liu H., Guo S., Xu Y., Li C., Zhang Z., Zhang D., Xu S., Zhang C., Chong K. (2014) OsmiR396d‐regulated OsGRFs function in floral organogenesis in rice through binding to their targets OsJMJ706 and OsCR4. Plant Physiol., 165: 160– 174. Liu S.C., Jin J.Q., Ma J.Q., Yao M.Z., Ma C.L., Li C.F., Ding Z.T., Chen L. (2016) Transcriptomic analysis of tea plant responding to drought stress and recovery. PLoS ONE, 11(1): e0147306. Liu X., Hu P., Huang M., Tang Y., Li Y., Li L., Hou X. (2016). The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat. Commun. 7: 12768. Lu C., Jeong D.H., Kulkarni K., Pillay M., Nobuta K., German R., Thatcher S.R., Maher C., Zhang L., Ware D., Liu B., Cao X., Meyers B.C., Green P.J. (2008) Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAS (nat-miRNAs). Proc Natl Acad Sci USA., 105: 4951-4956. Lu S.X., Knowles S.M., Andronis C., Ong M.S., Tobin E.M. (2012) CCA1 and ELF3 interact in the control of hypocotyl length and flowering time in Arabidopsis. Plant Physiol., 158: 1079-1088 Lv D.K., Bai X., Li Y., Ding X.D., Ge Y., Cai H., Ji W., Wu N., Zhu Y.M. (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene, 459 (1–2): 39-47. Macovei A., Garg B., Raikwar S., Balestrazzi A., Carbonera D., Buttafava A., . . . Tuteja, N. (2014). Synergistic Exposure of Rice Seeds to Different Doses of gamma-Ray and Salinity Stress Resulted in Increased Antioxidant Enzyme Activities and Gene-Specific Modulation of TC-NER Pathway. Biomed Research International, 676934, 15. Macovei A., Garg B., Raikwar S., Balestrazzi A., Carbonera D., Buttafava A., Tuteja N. (2014) Synergistic exposure of rice seeds to different doses of gamma-ray and salinity stress resulted in increased antioxidant enzyme activities and gene-specific modulation of TC-NER pathway. Biomed. Res. Int., 1-15. Macovei A., Tuteja N. (2012) microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.). BMC Plant Biology, 12: 183. Macovei A., Tuteja N. (2013) Different expression of miRNAs targeting helicases in rice in response to low and high dose rate γ-ray treatments. Plant Signal Behav., 8 (8): e25128. Maity J. P., Mishra D., Chakraborty A., Saha A., Santra S. C., Chanda S. (2005) Modulation of some quantitative and qualitative characteristics in rice (Oryza sativa L.) and mung (Phaseolus mungo L.) by ionizing radiation. Radiation Physics and Chemistry, 74(5): 391-394. Mangrauthia S.K., Bhogireddy S., Agarwal S., Prasanth V.V., Voleti S.R., Neelamraju S., Subrahmanyam D. (2017). Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars. J. Exp. Bot., 68: 2399–2412. Marcu D., Damian G., Cosma C., Cristea V. (2013b). Gamma radiation effects on seed germination, growth and pigment content, and ESR study of induced free radicals in maize (Zea mays). Journal of Biological Physics, 39(4): 625-634. Marcu D., Cristea V., Darban L. (2013a) Dose-dependent effects of gamma radiation on lettuce (Lactuca sativa var. capitata) seedlings. Int. J. Radiat. Biol., 89: 219-223. Martinez J., Patkaniowska A., Urlaub H., Luhrmann R., Tuschl T. (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110: 563-574. Martinez V., Del Amor F.M., Marcelis L.F.M. (2005) Growth and physiological response of tomato plants to different periods of nitrogen starvation and recovery. J. Hortic. Sci. Biotechnol., 80 (1): 147–153. Mecchia M.A., Debernardi J.M., Rodriguez R.E., Schommer C., Palatnik, J.F. (2013) MicroRNA miR396 and RDR6 synergistically regulate leaf development. Mech. Dev., 130: 2–13. Meijer H.A., Smith E.M., Bushell M. (2014) Regulation of miRNA strand selection: follow the leader? Biochem Soc Trans., 42:1135–40. Mi S., Cai T., Hu Y., Chen Y., Hodges E., Ni F., Wu L., Li S., Zhou H., Long C., Chen S., Hannon G.J., Qi Y. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell, 33: 116–27. Mittal D., Sharma N., Sharma V., Sopory S. K., Sanan-Mishra N. (2016). Role of microRNAs in rice plant under salt stress. Ann. Appl. Biol., 168: 2–18. Mittler R. (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci., 7: 405-410 Mittler R. (2016) ROS are good. Trends Plant Sci., 22: 11-19. Mittler R., Blumwald E. (2015) The roles of ROS and ABA in systemic acquired acclimation. Plant Cell, 27(1): 64-70. Mittler R., Vanderauwera S., Gollery M. and Van Breusegem, F. (2004) Reactive oxygen gene network of plants. Trends Plant Sci., 9: 490-498. Momiyama M., Koshiba T., Furukawa K., Kamiya Y., Satô M. (1999) Effects of gamma irradiation on elongation and indole3-acetic acid level of maize (Zea mays) coleoptiles. Environ. Exp. Bot., 41: (2): 131-143. Montes R.A., de Fatima R-C.F., De Paoli E., Accerbi M., Rymarquis L.A., Mahalingam G., Marsch-Martínez N., Meyers B.C., Green P.J., de Folter S. (2014) Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun., 5:3722. Montgomery T.A., Howell M.D., Cuperus J.T., Li D.W., Hansen J.E., Alexander A.L., Chapman E.J., Fahlgren N., Allen E., Carrington J.C. (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell, 133: 128–141. Moreira-Vilar F.C., Siqueira-Soares Rde C., Finger-Teixeira A., de Oliveira D.M., Ferro A.P., da Rocha, G.J., Ferrarese Mde L, dos Santos WD., Ferrarese-Filho O. (2014) The acetyl bromide method is faster, simpler and presents best recovery of lignin in different herbaceous tissues than Klason and thioglycolic acid methods. PLoS One, 9(10): e110000. Morozumi Y., Ino R., Ikawa S., Mimida N., Shimizu T., Toki S., Ichikawa H., Shibata T., Kurumizaka, H. (2013) Homologous pairing activities of two rice RAD51 proteins, RAD51A1 and RAD51A2. PLoS One, 8(10): e75451. Motomura K., Le Q.T., Kumakura N., Fukaya T., Takeda A. Watanabe Y. (2012) The role of decapping proteins in the miRNA accumulation in Arabidopsis thaliana. RNA Biol., 9: 644–652. Moura J.C., Bonine C.A., de Oliveira Fernandes Viana J., Dornelas M.C., Mazzafera P. (2010) Abiotic and biotic stresses and changes in the lignin content and composition in plants. J Integr Plant Biol., 52(4): 360-376. Moussa H. (2008) Gamma irradiation effects on antioxidant enzymes and G6PDH activities in Vicia faba plants J. New Seeds, 9(1): 89-99. Mu J, Tan H, Hong S, Liang Y, Zuo J. (2013) Arabidopsis transcription factor genes NF-YA1, 5, 6, and 9 play redundant roles in male gametogenesis, embryogenesis, and seed development. Mol Plant, 6(1): 188–201. Munné-Bosch S., Alegre L. (2002) The Function of Tocopherols and Tocotrienols in Plants. CRC Crit Rev Plant Sci., 21: 31-57. Mutum R.D., Kumar S., Balyan S., Kansal S., Mathur S., Raghuvanshi S. (2016) Identification of novel miRNAs from drought tolerant rice variety Nagina 22. Sci. Rep., 6: 30786. Nagata T., Yamada H., Du Z.J., Todoriki S., Kikuchi S., (2005) Microarray analysis of genes that respond to gamma-irradiation in Arabidopsis. J Agric Food Chem., 53: 1022–1030. Nihei T., Tanoi K., Nakanishi T.M. (2015) Inspection of Radiocesium Concentration Levels in Rice from Fukushima Prefecture after the Fukushima Dai-ichi Nuclear Power Plant Accident. Sci. Rep. 5, 8653. Nischal L., Mohsin M., Khan I., Kardam H., Wadhwa A., Abrol Y.P., Iqbal M., Ahmad A. (2012) Identification and comparative analysis of microRNAs associated with low-N tolerance in rice genotypes. PLoS One, 7(12): e50261. Nodine M.D., Bartel D.P. (2010) MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev., 24: 2678–269 O’ Brien J., Hayder H., Zayed Y., Peng C. (2018) Overview of MicroRNA biogenesis, mechanisms of actions, and circulation. Front Endocrinol., 9: 402. O'Toole N., Hattori M., Andres C., Iida K., Lurin C., Schmitz-Linneweber C., Sugita M., Small I. (2008) On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol., 25: 1120-1128. Panoli A.P., Ravi M., Sebastian J., Nishal B., Reddy T.V., Marimuthu M.P., Subbiah V., Vijaybhaskar V., Siddiqi I. (2006) AtMND1 is required for homologous pairing during meiosis in Arabidopsis. BMC Mol Biol., 7: 24. Paradiz J., Škrk J., Druškovic B. (1992) Cytogenetic effects of ionizing radiation on meristem. Acta Pharm., 42: 397-40. Park M.J., Kwon Y.J., Gil K.E., Park C.M. (2016) LATE ELONGATED HYPOCOTYL regulates photoperiodic flowering via the circadian clock in Arabidopsis. BMC Plant Biology, 20: 114. Park M.Y., Wu G., Gonzalez-Sulser A., Vaucheret H., Poethig R.S. (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. USA, 102: 3691–3696. Passardi F., Penel C., Dunand C. (2004) Performing the paradoxical: how plant peroxidases modify the cell wall. Trends Plant Sci., 9(11): 534-540. Passardi F., Cosio C., Penel C., Dunand C. (2005) Peroxidases have more functions than a Swiss army knife. Plant Cell Rep., 24: 255-265. Pencik A., Simonovik B., Petersson S.V., Henykova E., Simon S., Greenham K., Zhang Y., Kowalczyk M., Estelle M., Zazimalova E., Novak O., Sandberg G., Ljung K. (2013) Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell, 25: 3858–3870. Petroni K., Kumimoto R. W., Gnesutta N., Calvenzani V., Fornari M., Tonelli C., Holt B.F. 3rd, Mantovani R. (2012) The promiscuous life of plant NUCLEAR FACTOR Y transcription factors. Plant Cell, 24: 4777–4792. Phillips J.R., Dalmay T., Bartels D. (2007) The role of small RNAs in abiotic stress. Febs Lett., 581: 3592–3597. Piršelová B., Matušíková I. (2013) Callose: the plant cell wall polysaccharide with multiple biological functions. Acta Physiol. Plant, 35: 635–644. Pouget J.P., Frelon S., Ravanat J.L., Testard I., Odin F., Cadet J. (2002) Formation of modified DNA bases in cells exposed to either gamma radiation or high-LET particles. Radiat. Res., 157: 589-595. Pravalie R. (2014) Nuclear weapons tests and environmental consequences: a global perspective. AMBIO, 43: 729-744. Pysh L.D., Wysocka-Diller J.W., Camilleri C., Bouchez D., Benfey P.N. (1999) The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J., 18: 111–119. Qi W., Zhang L., Feng W., Xu H. Wang L., Jiao Z. (2015) ROS and ABA signaling are involved in the growth stimulation induced by low-dose gamma irradiation in Arabidopsis seedling. Appl. Biochem. Biotechnol., 175: 1490-1506. Raghuram B., Sheikh A.H., Sinha A.K. (2014) Regulation of MAP kinase signaling cascade by microRNAs in Oryza sativa. Plant signaling and behavior, 9: e972130. Raja V., Majeed U., Kang H., Andrabi K.I., John R. (2017) Abiotic stress: Interplay between ROS, hormones and MAPKs. Environmental and Experimental Botany, 137: 142-157. Rakwal R., Agrawal G.K., Shibato J., Imanaka T., Fukutani S., Tamogami S., Endo S., Sahoo S.K., Masuo Y., Kimura S. (2009) Ultra low-dose radiation: stress responses and impacts using rice as a grass model. Int J Mol Sci., 10: 1215–1225. Rakwal R., Kimura S., Shibato J., Nojima K., Kim Y.K., Nahm B.H., Jwa N.S., Endo S., Tanaka K., Iwahashi H. (2008) Growth retardation and death of rice plants irradiated with carbon ion beams is preceded by very early dose- and time-dependent gene expression changes. Mol Cells, 25: 272-278. Raman S., Greb T., Peaucelle A., Blein T., Laufs P., Theres K. (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. Plant J., 55: 65–76. Real A., Sundell-Bergman S., Knowles J.F., Woodhead D.S., Zinger I. (2004) Effects of ionizing radiation exposure on plants, fish and mammals: relevant data for environmental radiation protection. J Radiol Protection, 24: A123–A137. Reisz J.A., Bansal N., Qian J., Zhao W., Furdui C.M. (2014) Effects of ionizing radiation on biological molecules-mechanisms of damage and emerging methods of detection. Antioxid. Redox Signal., 21: 260-292. Remans T., Keunen E., Bex G.J., Smeets K., Vangronsveld J., Cuypers A. (2014). Reliable gene expression analysis by reverse transcription-quantitative PCR: reporting and minimizing the uncertainty in data accuracy. Plant Cell, 26(10): 3829-3837. Reyes J.L., Chua N.H. (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J., 49: 592–606. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. (2002) Prediction of plant microRNA targets. Cell, 110: 513–520. Rieu I., Ruiz‐Rivero O., Fernandez‐Garcia N., Griffiths J., Powers S.J., Gong F., Linhartova T., Eriksson S., Nilsson O., Thomas S.G., Phillips A.L., Hedden P. ( 2007) The gibberellin biosynthetic genes AtGA20ox1 and AtGA20ox2 act, partially redundantly, to promote growth and development throughout the Arabidopsis life cycle. The Plant Journal, 55: 488– 504. Rittenberg D., Foster L. (1940) A new procedure for quantitative analysis by isotope dilution, with application to the determination of amino acids and fatty acids. J. Biol. Chem., 133: 727–744. Robinson M.D., McCarthy D.J., Smyth G.K. (2010) EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, pp. 139-140. Rodriguez R.E., Ercoli M.F., Debernardi J.M., Breakfield N.W., Mecchia M.A., Sabatini M., Cools T. De Veylder L., Benfey P.N., Palatnik J.F. ( 2015) MicroRNA miR396 regulates the switch between stem cells and transit‐amplifying cells in Arabidopsis roots. Plant Cell, 27, 3354– 3366. Rogers K., Chen X. (2013) Biogenesis, turnover, and mode of action of plant MicroRNAs. Plant Cell, 25: 2383–2399. Rojas C.M., Senthil-Kumar M., Tzin V., Mysore K.S. (2014) Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Front. Plant Sci. 5: 17. Ros Barceló A. (1997) Lignification in plant cell walls. Intern. Rev. Cytol, 176: 87-132. RStudio. (2015) Integrated Development for R. RStudio, Inc, Boston, MA. Sade N., Del Mar Rubio-Wilhelmi M., Umnajkitikorn K., Blumwald E. (2017) Stress-induced senescence and plant tolerance to abiotic stress. J. Exp. Bot., 69: 845–853. Saha J., Brauer E.K., Sengupta A., Popescu S.C., Gupta K., Gupta B. (2015) Polyamines as redox homeostasis regulators during salt stress in plants. Front. Environ. Sci., 3, pp. 1-13. Sahr T., Voigt G., Schimmack W., Paretzke H.G., Ernst D. (2005) Low-level radiocaesium exposure alters gene expression in roots of Arabidopsis. New Phytologist, 168: 141-48. Sakaram S., Craig M.P., Hill N.T., Aljagthmi A., Garrido C., Paliy O., Bottomley M., Raymer M., Kadakia M.P. (2018) Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline. Scientific reports, 8(1):10069. Sancar A., Lindsey-BoltzL A., Unsal-Kacmaz K. and Linn S. (2004) Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annual Review of Biochemistry, 73: 39-85. Sax K. (1963) The stimulation of plant growth by ionizing radiation. Rad Bot., 3: 179–186. Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carre I.A., Coupland G. (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell, 93: 1219–1229. Secco D., Wang C., Shou H., Schultz M.D., Chiarenza S., Nussaume L., Lister R. (2015) Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife 4. Sharma P., Jha A.B., Dubey R.S., Pessarakli M. (2012). Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. J. Bot., 8: e23681. Shechter D., Constanzo V., Gautier J. (2004) Regulation of DNA replication by ATR: signalling in response to DNA intermediates. DNA Repair, 3: 901– 908. Shigenaga A.M., Argueso C.T. (2016) No hormone to rule them all: Interactions of plant hormones during the responses of plants to pathogens. Seminars in Cell and Developmental Biology, 56: 174-189. Shukla L.I., Chinnusamy V., Sunkar R. (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta, 1779: 743–748. Sidler C., Li D.P., Kovalchuk O., Kovalchuk I. (2015) Development-Dependent Expression of DNA Repair Genes and Epigenetic Regulators in Arabidopsis Plants Exposed to Ionizing Radiation. Radiation Research, 183: 219-32. Sieber P., Wellmer F., Gheyselinck J., Riechmann J.L., Meyerowitz E.M. (2007) Redundancy and specialization among plant miRNAs: Role of the MIR164 family in developmental robustness. Development, 134: 1051-1060. Šimura J., Antoniadi I., Široká J., Tarkowská D., Strnad M., Ljung K., Novák O. (2018) Plant hormonomics: multiple phytohormone profiling by targeted metabolomics. Plant Physiol., 177(2):476–489. Siriwardana C.L., Kumimoto, R.W., Jones, D.S., Holt, B.F. 3rd. (2014) Gene family analysis of the Arabidopsis NF-YA transcription factors reveals opposing abscisic acid responses during seed germination. Plant Mol. Biol. Report. 32: 971–986. Smirnoff N. (2000) Ascorbate biosynthesis and function in photoprotection - Discussion, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 355: 1464-64. Smith J.T., Willey N.J., Hancock J.T. (2012) Low dose ionizing radiation produces too few reactive oxygen species to directly affect antioxidant concentrations in cells. Biol. Lett., 8: 594–597. Song J., Keppler B., Wise R., Bent A. (2015) PARP2 is the predominant Poly(ADP-Ribose) polymerase in Arabidopsis DNA damage and immune responses. PLoS Genet., 11: e1005200. Song Y.H., Smith R.W., To B.J., Millar A.J., Imaizumi T. (2012) FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science, 336: 1045-1049. Sparrow A.H. (1965) Relationship between chromosome volume and radiation sensitivity in plant cells. Baltimore, Williams and Wilkins, 1965: 199–218 Sparrow A.H., Schwemmer S.S., Bottino P.J. (1971) The effects of external gamma radiation from radioactive fallout on plants with special reference to crop production. Radiat. Bot., 11: 85-118. Sparrow R.C., Sparrow A.H. (1965) Relative radiosensitivities of woody and herbaceous spermatophytes. Science 147: 1449–1451. Stajkov G., Ivanov K., Antonov M. (1986) Study of the growth, physiological-biological and productive changes in soybeans due to gamma radiation. Fiziol. Rast. 12(1): 65-74. Steinhauser G., Brandl A., Johnson T.E. (2014) Comparison of the Chernobyl and Fukushima nuclear accidents: A review of the environmental impacts. Science of The Total Environment, 470-471: 800-817. Stief A., Altmann S., Hoffmann K., Pant B.D., Scheible W.R., Baurle I. (2014) Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell, 26: 1792–1807. Stintzi A., Browse J. (2000) The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis. Proc. Natl. Acad. Sci. U.S.A. 97: 10625–10630. Streitner C., Danisman S., Wehrle L., Schöning J.C., Alfano J.R., Staiger D. (2008) The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana. Plant J., 56: 239-250. Subburaj S., Ha H.J., Jin Y.T., Jeon Y., Tu L., Kim J-B., Kang S.Y., Lee G.J. (2017) Identification of γ-radiation-responsive microRNAs and their target genes in Tradescantia (BNL clone 4430). J Plant Biol., 60: 116–128. Sun T., Zhang Y., Li Y., Zhang Q., Ding Y., Zhang Y. (2015) ChIP-seq reveals broad roles of SARD1 and CBP60g in regulating plant immunity. Nat Commun., 6: 10159. Sunkar R., Kapoor A., Zhu J.K. (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18: 2051-2065. Sunkar R., Li Y.F., Jagadeeswaran G. (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci., 17: 196–203. Sunkar R., Zhou X., Zheng Y., Zhang W., Zhu J.K. (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol., 8: 25. Suzuki N., Koussevitzky S., Mittler R., Miller G. (2012) ROS and redox signalling in the response of plants to abiotic stress. Plant Cell Environ., 35(2): 259-270. Syomov A.B., Ptitsyna S.N., Sergeeva S.A. (1992) Analysis of DNA strand break induction and repair in plants from the vicinity of Chernobyl. Sci. Total Environ., 112: 1-8. Sztatelman O., Grzyb J., Gabryś H., Banaś A.K. (2015) The effect of UV-B on Arabidopsis leaves depends on light conditions after treatment. BMC Plant Biol., 15: 281. Tabasum A., Cheema A.A., Hameed A., Rashid M., Ashraf M. (2011) Radio sensitivity of rice genotypes to gamma radiations based on seedling traits and physiological indices. Pakistan Journal of Botany, 43(2): 1211-1222. Takeda A., Iwasaki S., Watanabe T., Utsumi M., Watanabe Y. (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol., 49: 493–500. Takeno K. (2016) Stress-induced flowering: the third category of flowering response. Journal of Experimental Botany, 67 (17): 4925–4934. Tamburino R., Vitale M., Ruggiero A., Sassi M., Sannino L., Arena S., Costa A., Batelli G., Zambrano N., Scaloni A., Grillo S., Scotti N. (2017) Chloroplast proteome response to drought stress and recovery in tomato (Solanum lycopersicum L.). BMC Plant Biol., 17: 40. Tamura K., Adachi Y., Chiba K., Oguchi K., Takahashi H. (2002) Identification of Ku70 and Ku80 homologues in Arabidopsis thaliana: evidence for a role in the repair of DNA double‐strand breaks. Plant J., 29: 771–81. Tanaka A., Kobayashi Y., Hase Y., Watanabe H. (2002) Positional effect of cell inactivation on root gravitropism using heavy-ion microbeams. J. Exp. Bot., 53: 683-687. Teixeira F.K., Menezes-Benavente L., Margis R., MargisPinheiro M. (2004) Analysis of the molecular evolutionary history of the ascorbate peroxidase gene family: inferences from the rice genome. Journal of Molecular Evolution 59: 761–770. Tenhaken R. (2015). Cell wall remodeling under abiotic stress. Frontiers in Plant Science, 5: 771. Tian C., Wan P., Sun S., Li J., Chen M. (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol., 54: 519–532. Tian T., Liu Y., Yan H., You Q., Yi X., Du Z., Xu W., Su Z. (2017) agriGO v2.0: a GO analysis toolkit for the gricultural community, 2017 update. Nucleic Acids Res., 45: W122–W129. Trindade I., Capitao C., Dalmay T., Fevereiro M.P., Santos D.M. (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta, 231(3): 705–16. Truman W., Glazebrook J. (2012). Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation. BMC Plant Bio 12, 216. Tuteja N., Singh M.B., Misra M.K., Bhalla P.L., Tuteja R. (2001) Molecular mechanisms of DNA damage and repair: progress in plants. Crit. Rev. Biochem. Mol. Biol., 36 (4): 337-397. Tuteja N., Ahmad P., Panda B.B., Tuteja R. (2009) Genotoxic stress in plants: Shedding light on DNA damage, repair and DNA repair helicases. Mutat. Res., 681: 134-149. United States Environmental Protection Agency (USEPA). (2008) Technologically Enhanced Naturally Occurring Radioactive Materials from Uranium Mining. Volume 1: Mining and Reclamation background. Volume 2: Investigation of Potential Health, Geographic, and Environmental Issues of Abandoned Uranium Mines. UNSCEAR. (1996) Sources and effects of ionizing radiation. UNSCEAR 1996 Report to the General Assembly with Scientific Annex. UNSCEAR. (2008) Report to the general assembly with scientific annexes: Sources and effects of ionizing radiation. In, 245. New York: United Nations Scientific Committee on the Effects of Atomic Radiation. van de Walle J., Horemans N., Saenen E., Van Hees M., Wannijn J., Nauts R., van Gompel A., Vangronsveld J., Vandenhove H., Cuypers A. (2016). Arabidopsis plants exposed to gamma radiation in two successive generations show a different oxidative stress response. J Environ Radioact., 165: 270-279. Van Der Stricht E., Kirchmann R. (2001) Radioecology: radioactivity and ecosystems. International Union of Radioecology, Liège, Belgium. Van Hoeck A., Horemans N., Nauts R., Van Hees M., Vandenhove H., Blust R. (2017) Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies. Plant Sci., 257: 84–95. Van Hoeck A., Horemans N., Van Hees M., Nauts R., Knapen D., Vandenhove H., Blust R. (2015) Characterizing dose response relationships: chronic gamma radiation in Lemna minor induces oxidative stress and altered polyploidy level. J. Environ. Radioact., 150: 195–202. van Loon, L. C. (2016). The Intelligent Behavior of Plants. Trends Plant Sci., 21(4): 286-294. Vandenhove H., Vanhoudt N., Cuypers A., van Hees M., Wannijn J., Horemans N. (2010) Life-cycle chronic gamma exposure of Arabidopsis thaliana induces growth effects but no discernible effects on oxidative stress pathways. Plant Physiol Biochem., 48(9): 778-786. Vanhoudt N., Horemans N., Wannijn J., Nauts R., Van Hees M., Vandenhove H. (2014) Primary stress responses in Arabidopsis thaliana exposed to gamma radiation. J. Environ. Radioact., 129: 1–6. Vanhoudt N., Vandenhove H., Smeets K., Remans T., Van Hees M., Wannijn J., Cuypers A. (2008) Effects of uranium and phosphate concentrations on oxidative stress related responses induced in Arabidopsis thaliana. Plant Physiol. Biochem., 46 (11): 987-996. Vaucheret H., Vazquez F., Crete P., Bartel D.P. (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev., 18: 1187–1197. Vaucheret H. (2009). AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b. PLoS One, 4(7): e6442. Vaucheret H., Mallory A.C., Bartel D.P. (2006). AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol. Cell, 7;22(1): 129-36. Vazquez F., Blevins T., Ailhas J., Boller T., Meins F. Jr. (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res., 36(20): 6429–6438. Vazquez F., Legrand S., Windels D. (2010) The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci., 15: 337–345. Verkest A., Manes C.L., Vercruysse S., Maes S., Van Der Schueren E., Beeckman T., Genschik P., Kuiper M., Inzé D., De Veylder L. (2005) The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes. The Plant Cell, 17: 1723–1736. Verma V., Ravindran P., Kumar P.P. (2016) Plant hormone-mediated regulation of stress responses. BMC Plant Biol., 16: 86. Vick B.A., Zimmermann D.C. (1983) The biosynthesis of jasmonic acid: A physiological role for plant lipooxygenase. Biochem. Biophys. Res. Commun., 111: 470–477. Vinson D.S., Vengosh A., Hirschfeld D., Dwyer G.S. (2009) Relationships between radium and radon occurrence and hydrochemistry in fresh groundwater from fractured crystalline rocks, North Carolina (USA). Chemical Geology, 260: 159-171. Voinnet O. (2009) Origin, biogenesis, and activity of plant microRNAs. Cell, 136: 669-687. Volkova P.Y., Geras’kin S.A., Kazakova E.A. (2017) Radiation exposure in the remote period after the Chernobyl accident caused oxidative stress and genetic effects in Scots pine populations. Sci. Rep., 7: 43009. Vriezen W.H., Hulzink R., Mariani C., Voesenek L.A.C.J. (1999) 1-Aminocyclopropane-1-carboxylate oxidase activity limits ethylene biosynthesis in Rumex palustris during submergence. Plant Physiology, 121: 189–195. Wada H., Koshiba T., Matsui T., Sato M. (1998) Involvement of peroxidase in differential sensitivity to radiation in seedlings of two Nicotiana species. Plant Sci., 132: 109-19. Wang B., Sun Y.F., Song N., Wang X.J., Feng H., Huang L.L., Kang Z.S. (2013) Identification of UV-B-induced microRNAs in wheat. Genet. Mol. Res. 12: 4213-4221. Wang H., Mu X., He H., Zhang X.D. (2018) Cancer Radiosensitizers. Trends Pharmacol Sci., 39(1): 24-48. Wang J.W. (2014) Regulation of flowering time by the miR156-mediated age pathway. J Exp Bot., 65: 4723–4730. Wang L., Tsuda K., Truman W., Sato M., Nguyen le V., Katagiri F., Glazebrook J. (2011) CBP60g and SARD1 play partially redundant critical roles in salicylic acid signaling. Plant J., 67(6): 1029-1041. Wang T., Xu W., Den C., Xu S., Li F., Wu Y., Wu L., Bian P. (2016) A pivotal role of the jasmonic acid signal pathway in mediating radiation-induced bystander effects in Arabidopsis thaliana. Mutat Res., 791-792: 1-9. Wang J.W., Czech B., Weigel D. (2009) miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell, 138: 738–749 Waśkiewicz A., Beszterda M., Goliński P. (2014) Nonenzymatic Antioxidants in Plants. In: Oxidative Damage to Plants: Antioxidant Networks and Signaling. Ahmad P. (eds.) Elseiver USA: 201-234. Wasternack C., Strnad M. (2016) Jasmonate signaling in plant stress responses and development−active and inactive compounds. New Biotechnol, 33: 604-613. Watanabe Y., Ichikawa S., Kubota M., Hoshino J., Kubota Y., Maruyama K., Fuma S., Kawaguchi I., Yoschenko V.I., Yoshida S. (2015) Morphological defects in native Japanese fir trees around the Fukushima Daiichi Nuclear Power Plant. Scientific Reports, 5: 13232. Weber H., Vick B.A., Farmer E.E. (1997) Dinor-oxo-phytodienoic acid: A new hexadecanoid signal in the jasmonate family. Proc. Natl. Acad. Sci. USA, 94: 10473–10478. West C., Waterworth W., Story G., Sunderland P., Jiang Q., Bray C. (2002) Disruption of the Arabidopsis AtKu80 gene demonstrates an essential role for AtKu80 protein in efficient repair of DNA double‐strand breaks in vivo. Plant J., 31: 517–528. Wi S.G., Chung B.Y., Kim J.S., Kim J.H., Baek M.H., Lee J.W. (2006) Localization of hydrogen peroxide in pumpkin (Cucurbita ficifolia Bouché) seedlings exposed to high-dose gamma ray. J Plant Biol., 49: 1–8. Wi S.G., Chung B.Y., Kim J.S., Kim J.H., Baek M.H., Lee J.W., Kim Y.S. (2007) Effects of gamma irradiation on morphological changes and biological responses in plants. Micron., 38(6): 553-564. Willekens H., Inzé D., Van Montagu M., Van Camp W. (1995) Catalases in plants. Mol. Breed., 1: 207-228. Wong M.L., Medrano J.F. (2005) Real-time PCR for mRNA quantitation. Biotechniques, 39(1): 75-85. Woo H.R., Masclaux-Daubresse C., Lim P.O. (2018) Plant senescence: how plants know when and how to die. Journal of Experimental Botany, 69: 715–718. Wu L., Zhang Q., Zhou H., Ni F., Wu X., Qi Y. (2009) Rice microRNA effector complexes and targets. Plant Cell, 21(11): 3421–35. Wu L., Zhou H., Zhang Q., Zhang J., Ni F., Liu C., Qi Y. (2010) DNA methylation mediated by a microRNA pathway. Mol Cell, 38(3): 465-475. Wu Y., Lv W., Hu L., Rao W., Zeng Y., Zhu L., He Y. He G. (2017) Identification and analysis of brown plant hopper‐responsive microRNAs in resistant and susceptible rice plants. Sci. Rep., 7: 8712. Xie K., Shen J., Hou X., Yao J., Li X., Xiao J, Xiong L. (2012) Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiol., 158: 1382–1394. Xie, Z., Lee, E., Lucas, J.R., Morohashi, K., Li, D., Murray, J.A.H., Sack F.D., Grotewoldet E. (2010) Regulation of cell proliferation in the stomatal lineage by the Arabidopsis MYB FOUR LIPS via direct targeting of core cell cycle genes. Plant Cell, 22: 2306–2321. Xu M.Y., Zhang L., Li W.W., Hu X.L., Wang M.B., Fa Y.L., Zhang C.Y., Wang L. (2014) Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana. J. Exp. Bot., 65: 89–101. Xue L.J., Zhang J.J., Xue H.W. (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res., 37(3): 916–30. Yadav V. (2016) Effect of gamma radiation on various growth parameters and biomass of Canscora decurrens Dalz. Int. J. Herb. Med., 4: 109–115. Yang G., Wu L., Chen L., Pei B., Wang Y., Zhan F., Wu Y., Yu Z. (2007) Targeted irradiation of shoot apical meristem of Arabidopsis embryos induces long-distance bystander/abscopal effects. Radiat. Res., 167: 298-305. Yang S.D., Seo P.J., Yoon H.K., Park C.M. (2011) The Arabidopsis NAC Transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD Genes. Plant Cell, 23: 2155–2168. Yang X., Li L., (2012) Analyzing the microRNA transcriptome in plants using deep sequencing data. Biology, 1: 297–310. Yeung E., van Vee, H., Vashish, D., Sobral Paiv, A.L., Humme, M., Rankenber, T., Sasidharan R. (2018) A stress recovery signaling network for enhanced flooding tolerance in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A,. 115 (26): e6085–e6094. Yin J., Bauerle T.L. (2017) A global analysis of plant recovery performance from water stress. Oikos, 126: 1377–1388. Yokoyama Y., Reyss J.L., Guichard F. (1977) Production of radionuclides by cosmic rays at mountain altitudes. Earth Planet. Sci. Lett., 36: 44-50. Yoschenko V.I., Kashparov V.A., Melnychuk M.D., Levchuk S.E., Bondar Y.O., Lazarev M., Yoschenko M.I., Farfán E.B., Jannik G.T. (2011). Chronic irradiation of Scots Pine trees (Pinus sylvestris) in the Chernobyl exclusion zone: dosimetry and radiobiological effects. Health Phys. 101: 393–408. Yoschenko V.I., Nanba K., Yoshida S., Watanabe Y., Takase T., Sato N., Keitoku K. (2016) Morphological abnormalities in Japanese red pine (Pinus densiflora) at the territories contaminated as a result of the accident at Fukushima Dai-Ichi Nuclear Power Plant. J Environmental Radioactivity, 165: 60–67. Yoshihara T., Amanuma M., Tsutsumi T., Okumura Y., Matsuura H., Ishihara A. (1996) Metabolism and transport of [2-14C] (±) jasmonic acid in potato plant. Plant Cell Physiol., 37: 586-590. Young R.E., (1965) Effect of ionizing radiation on respiration and ethylene production of avocado fruit. Nature, 205: 1113-1114. Yu N., Cai W.J., Wang S., Shan C.M., Wang L.J., Chen X.Y. (2010) Temporal control of trichome distribution by microRNA156-targeted SPL genes in Arabidopsis thaliana. Plant Cell, 22: 2322–2335 Zeeshan H.M., Lee G.H, Kim H.R., Chae H.J. (2016) Endoplasmic reticulum stress and associated ROS. Int. J. Mol. Sci., 17(3): 327. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., Anderson T.A. (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res., 15: 336-360. Zhang J., Zhang H., Srivastava A. K., Pan Y., Bai J., Fang J., Shi H., Zhu J.K. (2018) Knockdown of rice microRNA166 confers drought resistance by causing leaf rolling and altering stem xylem development. Plant Physiol., 176 : 2082–2094. Zhang J.W., Long Y., Xiao X.G., Pei X.W. (2017) Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff). Shoots and Roots. PloS one, 12: e0170330. Zhang L., Peng Y., Wei X., Dai Y., Yuan D., Lu Y., Pan Y., Zhu Z. (2014) Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. J. Exp. Bot., 65: 5989–6002. Zhang M., Liang S., Hang X., Xiang Y., Sun Y. (2011a) Identification of heavy-ion radiation-induced microRNAs in rice. Adv. Space Res. 47: 1054-1061. Zhang W., Gao S., Zhou X., Chellappan P., Chen Z., Zhou X., Zhang X., Fromuth N., Coutino G., Coffey M., Jin H. (2011b) Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol., 75 (1-2): 93-105. Zhang X., Lei L., Lai J., Zhao H., Song W. (2018) Effects of drought stress and water recovery on physiological responses and gene expression in maize seedlings. BMC Plant Biol., 18(1): 68. Zhang Y., Xu S., Ding P., Wang D., Cheng Y.T., He J., Gao M., Xu F., Li Y., Zhu Z., Li X., Zhang Y. (2010) Control of salicylic acid synthesis and systemic acquired resistance by two members of a plants pecific family of transcription factors. Proc. Natl. Acad. Sci. USA., 107: 18220–18225. | - |
| local.type.refereed | Non-Refereed | - |
| local.type.specified | Phd thesis | - |
| item.fulltext | With Fulltext | - |
| item.accessRights | Embargoed Access | - |
| item.contributor | KARIUKI, Jackline | - |
| item.fullcitation | KARIUKI, Jackline (2019) Understanding the biological responses to ionizing radiation in plants after exposure and recovery: molecular profiling of Arabidopsis thaliana and Oryza sativa. | - |
| item.embargoEndDate | 2024-10-17 | - |
| Appears in Collections: | Research publications | |
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