• Korean Journal of Microbiology
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• v.52 no.2
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• pp.148-156
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• 2016

This study examined effects of Enterobacter ludwigii SJR3 showing a high 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, on growth of tomato plant and its expression of stress-related genes under drought and salt stress. SJR3 strain was inoculated at $10^6cell/g$ soil to 4-week grown tomato plants, and drought and salt stresses were treated. After additional incubation for 1 week, root length, stem length, fresh weight and dry weight of tomato plants treated with SJR3 increased by 37.8, 37.2, 96.8 and 146.6%, respectively compared to those of uninoculated plants in drought stress environment, and they increased by 19.2, 25.4, 19.5, and 105.8%, respectively in salt stress environment. Proline content in tomato leaves increased significantly under stress conditions as one of a protecting substance against stresses, but proline contents in tomato treated with SJR3 decreased by 62.1 and 54.1%, respectively. Relative expression of genes encoding ACC oxidase, ACO1 and ACO4, ethylene response factor genes ERF1 and ERF4, and some other stress-related genes were examined from tomato leaves. Compared to the non-stressed tomato, expressions of all stress-related genes increased significantly in the stressed tomato, but gene expressions in the inoculated tomato were similar to those of no-stressed control tomato. Therefore, E. ludwigii SJR3 may play an important role in mitigating drought and salt stress in plants, and can increase productivity of crops under various abiotic stresses.

• Journal of Ginseng Research
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• v.44 no.2
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• pp.312-320
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• 2020

Background: Ginseng (Panax ginseng Meyer) is an essential source of pharmaceuticals and functional foods. Ginseng productivity has been compromised by high light (HL) stress, which is one of the major abiotic stresses during the ginseng cultivation period. The genetic improvement for HL tolerance in ginseng could be facilitated by analyzing its genetic and molecular characteristics associated with HL stress. Methods: Genome-wide analysis of gene expression was performed under HL and recovery conditions in 1-year-old Korean ginseng (P. ginseng cv. Chunpoong) using the Illumina HiSeq platform. After de novo assembly of transcripts, we performed expression profiling and identified differentially expressed genes (DEGs). Furthermore, putative functions of identified DEGs were explored using Gene Ontology terms and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Results: A total of 438 highly expressed DEGs in response to HL stress were identified and selected from 29,184 representative transcripts. Among the DEGs, 326 and 114 transcripts were upregulated and downregulated, respectively. Based on the functional analysis, most upregulated and a significant number of downregulated transcripts were related to stress responses and cellular metabolic processes, respectively. Conclusion: Transcriptome profiling could be a strategy to comprehensively elucidate the genetic and molecular mechanisms of HL tolerance and susceptibility. This study would provide a foundation for developing breeding and metabolic engineering strategies to improve the environmental stress tolerance of ginseng.

• 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.

• Toxicological Research
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• v.22 no.2
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• pp.87-93
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• 2006

The KFDA (Korea Food & Drug Administration) has performed a collaborative toxico-genomics project since 2003. Its aim is to construct a toxicologenomic database of 12 hepatotoxic compounds from mice livers. Phenylbutazone which is non-steroidal anti-inflammatory drug was assigned. It was administered at low (0.0238 mg/kg) and at high (0.238 mg/kg) dose (5 mice per group) orally to the postnatal 6 weeks ICR mice, then the serum and liver were collected at the indicated time (6, 24 and 72 h) after administration. Serum biochemical markers for liver toxicity were measured and histopathologic studies also were carried out. The gene expression profiling was carried out by using Applied Biosystems 1700 Full Genome Expression Mouse. The 2-way ANOVA was used to find genes that reflected phenylbutazone-induced acute toxicity or dose-dependant changes. By self-organization maps (SOM), we identified groups with unique gene expression patterns, some of them are supposed to be related to phenylbutazone induced toxicity, including lipid metabolism abnormality, oxidative stress, cell death and cytoskeleton destruction.

• Fisheries and Aquatic Sciences
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• v.19 no.4
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• pp.21.1-21.11
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• 2016

Background: The evaluation of suitable reference genes as normalization controls is a prerequisite requirement for launching quantitative reverse transcription-PCR (RT-qPCR)-based expression study. In order to select the stable reference genes in abalone Haliotis discus hannai tissues (gill and hepatopancreas) under heavy metal exposure conditions (Cu, Zn, and Cd), 12 potential candidate housekeeping genes were subjected to expression stability based on the comprehensive ranking while integrating four different statistical algorithms (geNorm, NormFinder, BestKeeper, and ${\Delta}CT$ method). Results: Expression stability in the gill subset was determined as RPL7 > RPL8 > ACTB > RPL3 > PPIB > RPL7A > EF1A > RPL4 > GAPDH > RPL5 > UBE2 > B-TU. On the other hand, the ranking in the subset for hepatopancreas was RPL7 > RPL3 > RPL8 > ACTB > RPL4 > EF1A > RPL5 > RPL7A > B-TU > UBE2 > PPIB > GAPDH. The pairwise variation assessed by the geNorm program indicates that two reference genes could be sufficient for accurate normalization in both gill and hepatopancreas subsets. Overall, both gill and hepatopancreas subsets recommended ribosomal protein genes (particularly RPL7) as stable references, whereas traditional housekeepers such as ${\beta}-tubulin$ (B-TU) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were ranked as unstable genes. The validation of reference gene selection was confirmed with the quantitative assay of MT transcripts. Conclusions: The present analysis showed the importance of validating reference genes with multiple algorithmic approaches to select genes that are truly stable. Our results indicate that expression stability of a given reference gene could not always have consensus across tissue types. The data from this study could be a good guide for the future design of RT-qPCR studies with respect to metal regulation/detoxification and other related physiologies in this abalone species.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.572-579
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• 2019

Background: Panax ginseng has been used in traditional medicine to strengthen the body and mental well-being of humans for thousands of years. Many elite ginseng cultivars have been developed, and ginseng cultivation has become well established during the last century. However, heat stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Methods: We sequenced the transcriptomes (RNA-Seq) of two ginseng cultivars, Chunpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression and gene ontology enrichment along with profiled chlorophyll contents were performed. Results: CP is more sensitive to heat stress than YP and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP than in YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll a/b-binding proteins, WRKY transcription factors, and fatty acid desaturase were predominantly responsive during heat stress and appeared to regulate photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcription levels for ribulose 1,5-bisphosphate carboxylase/oxygenase under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Conclusion: Our comprehensive genomic analysis reveals candidate loci/gene targets for breeding and functional studies related to developing high temperature-tolerant ginseng varieties.

• Nutrition Research and Practice
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• v.9 no.2
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• pp.137-143
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• 2015

BACKGROUND/OBJECTIVES: Mulberry leaves contain quercetin derivatives, which have the effects of reducing obesity and improving lipid and glucose metabolism in mice with obesity. It is not clear whether or not mulberry leaves can directly affect metabolic disorders, in the presence of obesity, because of the interaction between obesity and metabolic disorders. The aim of the current study was to assess the direct action of quercetin derivatives on metabolic disorders in non-obese conditions in short-term high-fat diet fed mice. MATERIALS/METHODS: C57BL/6N mice were fed a high-fat diet, supplemented with either 0% (control), 1%, or 3% mulberry leaf powder (Mul) or 1% catechin powder for five days. Anthropometric parameters and blood biochemistry were determined, and hepatic gene expression associated with lipid and glucose metabolism was analyzed. RESULTS: Body and white fat weights did not differ among the four groups. Plasma triglycerides, total cholesterol, and free fatty acids in the 1%, 3% Mul and catechin groups did not differ significantly from those of the controls, however, plasma glucose and 8-isoprostane levels were significantly reduced. Liver gene expression of gp91phox, a main component of NADPH oxidase, was significantly down-regulated, and PPAR-${\alpha}$, related to ${\beta}$-oxidation, was significantly up-regulated. FAS and GPAT, involved in lipid metabolism, were significantly down-regulated, and Ehhadh was significantly up-regulated. Glucose-metabolism related genes, L-PK and G6Pase, were significantly down-regulated, while GK was significantly up-regulated in the two Mul groups compared to the control group. CONCLUSIONS: Our results suggest that the Mul quercetin derivatives can directly improve lipid and glucose metabolism by reducing oxidative stress and enhancing ${\beta}$-oxidation. The 1% Mul and 1% catechin groups had similar levels of polyphenol compound intake ($0.4{\times}10^{-5}$ vs $0.4{\times}10^{-5}$ mole/5 days) and exhibited similar effects, but neither showed dose-dependent effects on lipid and glucose metabolism or oxidative stress.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.102-111
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• 2016

The goal of this study was to characterize the BrDSR (Drought Stress Resistance in B. rapa) gene and to identify the expression network of drought-inducible genes in Chinese cabbage under drought stress. Agrobacterium-mediated transformation was conducted using a B. rapa inbred line ('CT001') and the pSL100 vector containing the BrDSR full length CDS (438 bp open reading frame). Four transgenic plants were selected by PCR and the expression level of BrDSR was approximately 1.9-3.4-fold greater than that in the wild-type control under drought stress. Phenotypic characteristics showed that BrDSR over-expressing plants were resistant to drought stress and showed normal growth habit. To construct a co-expression network of drought-responsive genes, B. rapa 135K cDNA microarray data was analyzed to identify genes associated with BrDSR. BrDSR was directly linked to DARK INDUCIBLE 2 (DIN2, AT3G60140) and AUTOPHAGY 8H (ATG8H, AT3G06420) previously reported to be leaf senescence and autophagy-related genes in plants. Taken together, the results of this study indicated that BrDSR plays a significant role in enhancement of tolerance to drought conditions.

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.246-253
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• 2007

Doxorubicin and daunorubicin are excellent chemotherapeutic agents utilized for several types of cancer but the irreversible cardiac damage is the major limitation for its use. The biochemical mechanisms of doxorubicin- and daunorubicin- induced cardiotoxicity remain unclear. There are many reports on toxicity of doxorubicin and doxorubicin in cardiomyocytes, but effects in cardiovascular system by these drugs are almost not reported. In this study, we investigated gene expression profiles in human umbilical vein endothelial cells (HUVECs) to better understand the causes of doxorubicin and doxorubicininduced cardiovascular toxicity and to identify differentially expressed genes (DEGs). Through the clustering analysis of gene expression profiles, we identified 124 up-regulated common genes and 298 down-regulated common genes changed by more than 1.5-fold by all two cardiac toxicants. HUVECs responded to doxorubicin and doxorubicin damage by increasing levels of apoptosis, oxidative stress, EGF and lipid metabolism related genes. By clustering analysis, we identified some genes as potential markers on apoptosis effects of doxorubicin and doxorubicin. Six genes of these, BBC3, APLP1, FAS, TP53INP, BIRC5 and DAPK were the most significantly affected by doxorubicin and doxorubicin. Thus, this study suggests that these differentially expressed genes may play an important role in the cardiovascular toxic effects and have significant potential as novel biomarkers to doxorubicin and doxorubicin exposure.

• Food Science of Animal Resources
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• v.36 no.4
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• pp.469-475
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• 2016

This study examined the relationship between NaCl sensitivity and stress response of Listeria monocytogenes. Nine strains of L. monocytogenes (NCCP10805, NCCP10806, NCCP10807, NCCP10808, NCCP10809, NCCP10810, NCCP10811, NCCP10920 and NCCP 10943) were exposed to 0%, 1%, 2% and 4% NaCl, and then incubated at 60℃ for 60 min to select strains that were heat-sensitized (HS) and non-sensitized (NS) by NaCl exposure. After heat challenge, L. monocytogenes strains were categorized as HS (NCCP 10805, NCCP10806, NCCP10807, NCCP10810, NCCP10811 and NCCP10920) or NS (NCCP10808, NCCP10809 and NCCP10943). Total mRNA was extracted from a HS strain (NCCP10811) and two NS strains (NCCP10808 and NCCP10809), and then cDNA was prepared to analyze the expression of genes (inlA, inlB, opuC, betL, gbuB, osmC and ctc) that may be altered in response to NaCl stress, by qRT-PCR. The expression levels of two invasion-related genes (inlA and inlB) and two stress response genes (opuC and ctc) were increased (p<0.05) in NS strains after NaCl exposure in an NaCl concentration-dependent manner. However, only betL expression was increased (p<0.05) in the HS strains. These results indicate that the effect of NaCl on heat sensitization of L. monocytogenes is strain dependent and that opuC and ctc may prevent NS L. monocytogenes strains from being heat sensitized by NaCl. Moreover, NaCl also increases the expression of invasion-related genes (inlA and inlB).