• Journal of Radiation Industry
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• v.2 no.3
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• pp.111-119
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• 2008

Microarrays can measure the expression of thousands of genes to identify the changes in expression between different biological states. To survey the change of whole Salmonella genes after a relatively high dose of gamma radiation (1 kGy), transcriptome dynamics were examined in the cells by using DNA microarrays. At least 75 genes were induced and 89 genes were reduced two-fold or more after irradiation. Several genes located in pSLT plasmid, cyo operon, and Gifsy prophage were induced along with many genes encoding uncharacterized proteins.While, the expression of genes involved in the virulence of Salmonella as well as metabolic functions were decreased. Although the radiation response as a whole could not be illustrated by using DNA microarrays, the data suggest that the response to high dose of irradiation might be more complex than the SOS response.

• Journal of Radiation Industry
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• v.7 no.2_3
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• pp.109-113
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• 2013

In a previous study, a relatively high dose of gamma radiation (1 kGy) did not fully induce typical SOS genes such as sulA, recA, recN, and din in Salmonella Typhimurium (S. Typhimurium) (Lim et al. 2008, Gene expression profiles following high-dose exposure to gamma radiation in Salmonella enterica serovar Typhimuium. J. Radiat. Ind. 3:111-119). In this study, we examined changes in the transcriptional repertoire of S. Typhimurium after a dose of 10 Gy using DNA microarrays. It was found that more than half (~65%) of the 26 up-regulated genes belong to the SOS regulon: ten genes are typical SOS genes, and seven genes are Salmonella prophage genes, which are known to be activated by LexA cleavage. Among 29 down-regulated genes, the function of five genes with the most decreased expression is associated with carbohydrate transport and energy production. This suggests that upon exposure to gamma radiation cells may cease growing by reducing the metabolic activity, and repair DNA damage using a DNA repair system such as the SOS response system. The difference in expression of the SOS genes between a high (1 kGy) and low (10 Gy) dose of radiation shows the possibility that cells may opt for one of multiple regulatory circuits in response to the specific gamma radiation dose.

• Journal of Radiation Industry
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• v.4 no.3
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• pp.289-295
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• 2010

The bacterium Deinococcus radiodurans is one of the most resistant organisms to the effects of ionizing radiation and other DNA-damaging agents. In this study, distributions of 10 ddr (DNA damage response) genes were investigated in 8 species of Deinococcus by polymerase chain reaction (PCR). We have compared the sequences of ddr genes of D. radiodurans, D. geothermalis and D. deserti, and selected primers which are suitable for the detection of ddr in different species of Deinococcus. A sequence homology search and PCR assay showed that ddrO, which encodes a global regulator of the radiation-desiccation response, was most well conserved in the Deinococcus lineage.

• Journal of Radiation Protection and Research
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• v.40 no.1
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• pp.25-35
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• 2015

We analyzed the differential effects of histopathology, apoptosis and expression of radiation response genes after chronic low dose rate (LDR) and acute high dose rate (HDR) radiation exposure in spleen, lung and liver of rats. Female 6-week-old Sprague-Dawley rats were used. For chronic low-dose whole body irradiation, rats were maintained for 14 days in a $^{60}Co$ gamma ray irradiated room and received a cumulative dose of 2 Gy or 5 Gy. Rats in the acute whole body exposure group were exposed to an equal dose of radiation delivered as a single pulse ($^{137}Cs$-gamma). At 24 hours after exposure, spleen, lung and liver tissues were extracted for histopathologic examination, western blotting and RT-PCR analysis. 1. The spleen showed the most dramatic differential response to acute and chronic exposure, with the induction of substantial tissue damage by HDR but not by LDR radiation. Effects of LDR radiation on the lung were only apparent at the higher dose (5 Gy), but not at lower dose (2 Gy). In the liver, HDR and LDR exposure induced a similar damage response at both doses. RT-PCR analysis identified cyclin G1 as a LDR-responsive gene in the spleen of rats exposed to 2 Gy and 5 Gy gamma radiation and in the lung of animals irradiated with 5 Gy. 2. The effects of LDR radiation differed among lung, liver, and spleen tissues. The spleen showed the greatest differential effect between HDR and LDR. The response to LDR radiation may involve expression of cyclin G1.

• Korean Journal of Environmental Biology
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• v.23 no.2 s.58
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• pp.152-156
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• 2005

Ionizing radiation is a well- known therapy factor for human carcinoma cells. Genotoxic stress mediates cell cycle control, transcription and cellular signaling. In this work, we have used a microarray hybridization approach to characterize the cell type-specific transcriptional response of human carcinoma MCF-7 and HeLa cell line to $\gamma-radiation$, such as 4Gy 4hr. We found that exposure to $\gamma-ray$ alters by at least a $log_2$ factor of 1.0 the expression of known genes. Of the 27 genes affected by irradiation, 11 are down- regulated in MCF-7 cells and 2 genes induced by radiation,15 are repressed in HeLa cells. Many genes were involved in known damage- response pathways for cell cycling, transcription factor and cellular signaling response. However, in MCF-7 cells, we observed gene expression pattern in chromatin, apoptosis, stress, differentiation, cytokine, metabolism, ribosome and calcium. In HeLa cells, it showed clearly the expression changes in adhesion and migration, lysosome, brain, genome instability and translation. These insights reveal new therapy directions for studying the human carcinoma cell response to radiation.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.438-447
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• 2011

Deinococcus radiodurans is extremely resistant to various genotoxic conditions and chemicals. In this study, we characterized the effect of a sublethal concentration (100 ${\mu}M$) of cadmium (Cd) on D. radiodurans using a whole-genome DNA microarray. Time-course global gene expression profiling showed that 1,505 genes out of 3,116 total ORFs were differentially expressed more than 2-fold in response to Cd treatment for at least one timepoint. The majority of the upregulated genes are related to iron uptake, cysteine biosynthesis, protein disulfide stress, and various types of DNA repair systems. The enhanced upregulation of genes involved in cysteine biosynthesis and disulfide stress indicate that Cd has a high affinity for sulfur compounds. Provocation of iron deficiency and growth resumption of Cd-treated cells by iron supplementation also indicates that CdS forms in iron-sulfur-containing proteins such as the [Fe-S] cluster. Induction of base excision, mismatch, and recombinational repair systems indicates that various types of DNA damage, especially base excision, were enhanced by Cd. Exposure to sublethal Cd stress reduces the growth rate, and many of the downregulated genes are related to cell growth, including biosynthesis of cell membrane, translation, and transcription. The differential expression of 52 regulatory genes suggests a dynamic operation of complex regulatory networks by Cd-induced stress. These results demonstrate the effect of Cd exposure on D. radiodurans and how the related genes are expressed by this stress.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.29-44
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• 2001

DNA damage by physical insult including UV and g-radiation might provoke genetic alterations in cells, which is followed by either acute cell death or tumorigenesis. The responsiveness to g-radiation depends on cellular context of target cells. To understand the mechanisms of checkpoint control, repair and cell death following genotoxic stimu]i, cDNA microarray can provide the gene expression profile. To make a profile of gene expression in irradiated Jurkat T cells, we hybridized the cDNA microarray using cDNA from g-irradiated Jurkat T cells. Jurkat T cells were exposed to 4Gy to 16Gy, and total RNA were extracted at 4 to 24 hrs after irradiation. The hybridization of the microarray to fluorescence-labeled cDNA from treated and untreated cells was analyzed by bioinformatic analysis to address relative changes in expression levels of the genes present in the array. Responses varied widely in different time points, suggesting acute stress response and chronic restoration or cell death. From these results we could select 384 genes related to radiation response in Tcells, and radiation response might be different in various types of cells. Using Radchip, we could separate "the exposed" from control PBMCs. We propose that Radchip might be useful to check the radiation research as well as radiation carcinogenesis.

• Korean Journal of Environmental Biology
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• v.21 no.1
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• pp.52-55
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• 2003

There is considerable evidence that ionizing radiation (IR) mediates checkpoint control, repair and cell death. In this study, we have used a high density microarray hybridization approach to characterize the transcriptional response of human breast carcinoma MCF-7 cell line to ${\gamma}$-radiation, such as 4 Gy 4 hr, 8 Gy 4 hr, and 8 Gy 12 hr. We found that exposure to ${\gamma}$-ray alters by at least a $log_2$ factor of 1.0 the expression of 115 known genes. Of the 66 genes affected by ${\gamma}$-radiation, 49 are down-regulated. In our results, the cellular response to irradiation includes induction of the c-jun and EGR1 early response genes. The present work has examined potential cytoplasmic signaling cascades that transduce IR-induced signals to the nucleus. 40S ribosomal protein s6 kinase modulates the activities of the mitogen activated protein kinase (MAPK) and c-Jun $NH_2$-terminal kinase (JNK1) cascades in human monocytic leukemia (U937/pREP4) cells. 14-3-3 family members are dimeric phosphoserine -binding proteins that participate in signal transduction and checkpoint control pathways.

• Journal of Radiation Industry
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• v.4 no.4
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• pp.325-334
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• 2010

Transcriptional regulation in response to salt in mutant lines was investigated using oligonucleotide microarrays. In order to characterize the salt-responsive genes in rice, the expression profiles of transcripts that responded to salt-treatment were monitored using the microarrays. In the microarray analysis, among 37,299 reliable genes, 5,101, 2,758 and 2,277 genes were up-regulated by more than 2-fold using the salt treatment, while the numbers of down-regulated genes were 4,619, 3,234, and 1,878 in the WT, ST-495, and ST-532, respectively. From genotype changes induced by gamma ray mutagenesis, 3,345 and 2,397 genes were up-regulated, while 2,745 and 2,075 genes were down-regulated more than 2-fold in the two untreated mutants lines compared with untreated WT, respectively. A total of 3,108 and 2,731 genes were up-regulated more than 2-fold, while 3,987 and 3,660 genes were down-regulated by more than 2-fold in the salt treatment of the two mutants lines compared with the salt treated WT, respectively. The expressions of membrane transporter genes such as OsAKT1, OsKUP, and OsNAC increased more severely in ST-495 and ST-532 than in the WT. The expressions of the proline accumulation related genes such as OsP5CS and OsP5CR were also markedly increased in the salt tolerant mutants when compared to the WT plant.

• Korean Journal of Environmental Biology
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• v.22 no.3
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• pp.472-477
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• 2004

To study the radiation related gene expression in mutants of Bacillus lentimorbus WJ5 induced by gamm radiation, the simultaneous gene expression was analyzed by DNA micro array. We constructed DNA chips including two thousand randomly digested genome spots of B. lentimorbus WJ5 and compared its quantitative aspect with seven mutants induced by gamma radiation $(^{60}/Co)$. From the cluster analysis of gene expression pattern, totally 408 genes were expressed and 27 genes were significantly upregulated by the gamma radiation in all mutants. Especially, genes involved in repair (mutL, mutM), energy metabolism (acsA, sdhB, pgk, yhjB, citB), protease (npr), and reduction response to oxidative stress (HMM) were simultaneously upregulated. It seems that the induction of the direct and/or indirect repair related genes in mutants induced by gamma radiation could be remarkably different from the adaptive responses against acute exposure to radiation.