• Journal of The Korean Society of Grassland and Forage Science
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• v.35 no.3
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• pp.264-268
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• 2015

The present research investigated copper and cadmium stress-induced differentially expressed genes (DEGs) using annealing control primers (ACP) with the differential display reverse transcription polymerase chain reaction technique in alfalfa (Medicago sativa L. cv. Vernal) leaves. Alfalfa leaves were subjected to $250{\mu}M$ of copper and cadmium treatment for a period of 6 h. A total of 120 ACPs was used. During copper and cadmium treatment, 6 DEGs were found to be up or down regulated. During copper stress treatment, 1 DEG was up-regulated, and 3 novel genes were discovered. Similarly, during cadmium stress treatment, 1 DEG was up-regulated and 5 novel genes were identified. Among all 6 DEGs, DEG-4 was identified as the gene for trans-2,3-enoyl-CoA reductase, DEG-5 was identified as the gene for senescence-associated protein DIN1 and DEG-6 was identified for caffeic acid O-methyltransferase. All the up-regulated genes may play a role in copper and cadmium stress tolerance in alfalfa.

• Geomechanics and Engineering
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• v.33 no.3
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• pp.231-242
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• 2023

This paper represents a comparative study in which Gene Expression Programming (GEP), Group Method of Data Handling (GMDH), and multiple linear regressions (MLR) were utilized to derive new equations for the prediction of time-dependent bearing capacity of pile foundations driven in cohesive soil, technically called pile set-up. This term means that many piles which are installed in cohesive soil experience a noticeable increase in bearing capacity after a specific time. Results of researches indicate that side resistance encounters more increase than toe resistance. The main reason leading to pile setup in saturated soil has been found to be the dissipation of excess pore water pressure generated in the process of pile installation, while in unsaturated conditions aging is the major justification. In this study, a comprehensive dataset containing information about 169 test piles was obtained from literature reviews used to develop the models. to prepare the data for further developments using intelligent algorithms, Data mining techniques were performed as a fundamental stage of the study. To verify the models, the data were randomly divided into training and testing datasets. The most striking difference between this study and the previous researches is that the dataset used in this study includes different piles driven in soil with varied geotechnical characterization; therefore, the proposed equations are more generalizable. According to the evaluation criteria, GEP was found to be the most effective method to predict set-up among the other approaches developed earlier for the pertinent research.

• Journal of Microbiology and Biotechnology
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• v.23 no.9
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• pp.1293-1303
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• 2013

Antibiotic resistance of soilborne Acinetobacter species has been poorly explored. In this study, norfloxacin resistance of a soil bacterium, Acinetobacter oleivorans DR1, was investigated. The frequencies of mutant appearance of all tested non-pathogenic Acinetobacter strains were lower than those of pathogenic strains under minimum inhibitory concentration (MIC). When the quinolone-resistance-determining region of the gyrA gene was examined, only one mutant (His78Asn) out of 10 resistant variants had a mutation. Whole transcriptome analysis using a RNA-Seq demonstrated that genes involved in SOS response and DNA repair were significantly up-regulated by norfloxacin. Determining the MICs of survival cells after norfloxacin treatment confirmed some of those cells were indeed persister cells. Ten colonies, randomly selected from among those that survived in the presence of norfloxacin, did not exhibit increased MIC. Thus, both the low mutation frequency of the target gene and SOS response under norfloxacin suggested that persister formation might contribute to the resistance of DR1 against norfloxacin. The persister frequency increased without a change in MIC when stationary phase cells, low growth rates conditions, and growth-deficient dnaJ mutant were used. Taken together, our comprehensive approach, which included mutational analysis of the target gene, persister formation assays, and RNA sequencing, indicated that DR1 survival when exposed to norfloxacin is related not only to target gene mutation but also to persister formation, possibly through up-regulation of the SOS response and DNA repair genes.

• Journal of Nutrition and Health
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• v.53 no.4
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• pp.347-355
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• 2020

Purpose: Zinc is known to be associated with osteoblast proliferation and differentiation. Osterix as zinc-finger transcription factor is also related to osteoblast differentiation and bone formation. In the present study, we aimed to investigate whether zinc modulates osterix gene and protein expression in osteoblastic MC3T3-E1 cells. Methods: MC3T3-E1 cells were cultured in zinc-dependent concentrations (0, 0.5, 1, 5, or 15 µM Zn), along with osteogenic control (normal osteogenic medium) for 1 and 3 days. The gene and protein expression levels of osterix were analyzed by real-time reverse transcription polymerase chain reaction and Western blotting, respectively. Results: Zinc increased osteoblast proliferation in a concentration-dependent manner at day 1 and 3. Similarly, zinc increased the activity of osteoblast marker enzyme alkaline phosphatase in cells and media in a zinc concentration-dependent manner. Moreover, our results showed that the pattern of osterix gene expression by zinc was down-regulated within the low levels of zinc treatments (0.5-1 µM) at day 1, but it was up-regulated after extended culture period at day 3. Osterix protein expression by zinc showed the similar pattern of gene expression, which down-regulated by low zinc levels at day 1 and up-regulated back at day 3 as the early stage of osteoblast differentiation. Conclusion: Our results suggest that zinc modulates osterix gene and protein expression in osteoblasts, particularly in low level of zinc at early stage of osteoblast differentiation period.

• Molecular & Cellular Toxicology
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• v.2 no.4
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• pp.266-272
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• 2006

Carpal tunnel syndrome (CTS) is one of the most common disorders by under pressure of the median nerve at the wrist in these days. However, pathological mechanism of CTS is unknown. We carried out this study to identify the changes of gene expression and to evaluate possible mechanism in CTS. 120 CTS patients and 30 control patients were included in this study. Patients with a history of diabetes, hypertension, thyroid diseases, and arthritis were excluded. CTS patients were divided to three experimental groups-Mild, Moderate, and Severe group-according to elecrodiagnosis. Radioactive cDNA microarrays (Nylon membrane including 1,152 genes) were used to examine the difference of gene expression profile in CTS. We identified up-regulated genes by more than 2.0 value of z-ratio, and down-regulated genes by less than-2.0 value of z-ratio. 20 genes such as the ITGAL, ITGAM, PECAM1, VIL2, TGFBR2, RAB7, RNF5 and NFKB1 were up-regulated, and 28 genes such as PRG5, CASP8, CDH1, IGFBP5, CBX3, HREV107, PIN, and WINT2 were down-regulated. These genes were related with TGF beta signaling pathway, NF-Kb signaling pathway, antiapoptotic pathway and T cell receptor signaling pathway. However, there were no differences in gene expression profiles according to severities of symptoms. We suggest that CTS could be related with proinflammatory mechanism and antiapoptotic mechanism.

• Molecular & Cellular Toxicology
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• v.5 no.2
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• pp.99-107
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• 2009

Naphthalene is bicyclic aromatic compound that is widely used in various domestic and commercial applications including lavatory scent disks, soil fumigants and moth balls. Exposure to naphthalene results in the development of bronchiolar damage, cataracts and hemolytic anemia in humans and laboratory animals. However, little information is available regarding the mechanism of naphthalene toxicity. We investigated gene expression profiles and potential signature genes in human hepatocellular carcinoma HepG2 cells and human promyelocytic leukemia HL-60 cells after 3 h and 48 h incubation with the IC$_{20}$ and IC$_{50}$ of naphthalene by using 44 k agilent whole human genome oligomicroarray and operon human whole 35 k oligomicroarray, respectively. We identified 616 up-regulated genes and 2,088 down-regulated genes changed by more than 2-fold by naphthalene in HepG2 cells. And in HL-60, we identified 138 up-regulated genes and 182 down-regulated genes changed by more than 2-fold. This study identified several interesting targets and functions in relation to naphthalene-induced toxicity through a gene ontology analysis method. Apoptosis and cell cycle related genes are more commonly expressed than other functional genes in both cell lines. In summary, the use of in vitro models with global expression profiling emerges as a relevant approach toward the identification of biomarkers associated with toxicity after exposure to a variety of environmental toxicants.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.39 no.3
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• pp.112-119
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• 2013

Objectives: This study investigated the question of whether adenoviral magnetofection can be a suitable method for increasing the efficacy of gene delivery into bone marrow stromal cell (BMSC) and for generation of a high level of bone morphogenic protein (BMP) secretion at a minimized viral titer. Materials and Methods: Primary BMSCs were isolated from C57BL6 mice and transduced with adenoviral vectors encoding ${\beta}$ galactosidase or BMP2 and BMP7. The level of BMP secretion, activity of osteoblast differentiation, and cell viability of magnetofection were measured and compared with those of the control group. Results: The expression level of ${\beta}$ galactosidase showed that the cell transduction efficiency of AdLacZ increased according to the increased amount of magnetic nanoparticles. No change in cell viability was observed after magnetofection with 2 ${\mu}L$ of magnetic nanoparticle. Secretion of BMP2 or BMP7 was accelerated after transduction of AdBMP2 and 7 with magnetofection. AdBMP2 adenoviral magnetofection resulted in up to 7.2-fold higher secretion of BMP2, compared with conventional AdBMP2-transduced BMSCs. Magnetofection also induced a dramatic increase in secretion of BMP7 by up to 10-fold compared to the control. Use of only 1 multiplicity of infection (moi) of magnetofection with adenoviral transduction of AdBMP2 or AdBMP7 resulted in significantly higher transgene expression compared to 20 moi of conventional adenoviral transduction. Conclusion: Magnetic particle-mediated gene transudation is a highly efficient method of gene delivery to BMSCs. Magnetofection can lower the amount of viral particles while improving the efficacy of gene delivery.

• Biomedical Science Letters
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• v.13 no.4
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• pp.293-304
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• 2007

The emergence of extended spectrum $\beta$-lactamase (ESBL) producing bacteria is worldwide concern. Until recently, the most frequently identified strains in the Republic of Korea were E. coli and Klebsiella spp. The incidence of resistance to extended spectrum $\beta$-lactam antibiotics is increasing in Wonju city, Korea. Total 57 strains of ESBL producing E. coli and Klebsiella species were isolated from Wonju Christian Hospital during a 9 month-period from April to December, 2003. To determine the prevalence and genotypes of the ESBL producing clinical isolates, antibiotic susceptibility and ESBL activity test by VITEK system and double disk synergy (DDS) test, and PCR based genotyping were performed. Fourteen (82%) isolates of 17 ESBL producing E. coli were found to have $bla_{TEM}$ gene and 5 (29%) isolates were found to have $bla_{CTX-M}$ gene by polymerase chain reaction (PCR). Thirty (75%) isolates of 40 ESBL producing Klebsiella species with $bla_{TEM}$ gene, 38 (95%) isolates with $bla_{SHV}$ gene, and 7 (20%) isolates with $bla_{CTX-M}$ type gene were also identified. Enterobacterial repetitive intergenic consensus (ERIC) PCR and similarity index by dendrogram for genetical similarity to band pattern of each clinical isolates were examined. ESBL producing E. coli were grouped into 6 clusters up to 84% of similarity index and Klebsiella species were grouped into 12 clusters up to 76% of similarity index. In conclusion, ESBL producing clinical isolates were characterized with the results from antimicrobial resistance pattern and genetical similarity using ERiC PCR.

• The Plant Pathology Journal
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• v.29 no.2
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• pp.209-220
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• 2013

Root colonization by Pseudomonas chlororaphis O6 induces systemic drought tolerance in Arabidopsis thaliana. Microarray analysis was performed using the 22,800-gene Affymetrix GeneChips to identify differentially-expressed genes from plants colonized with or without P. chlororaphis O6 under drought stressed conditions or normal growth conditions. Root colonization in plants grown under regular irrigation condition increased transcript accumulation from genes associated with defense, response to reactive oxygen species, and auxin- and jasmonic acid-responsive genes, but decreased transcription factors associated with ethylene and abscisic acid signaling. The cluster of genes involved in plant disease resistance were up-regulated, but the set of drought signaling response genes were down-regulated in the P. chlororaphis O6-colonized under drought stress plants compared to those of the drought stressed plants without bacterial treatment. Transcripts of the jasmonic acid-marker genes, VSP1 and pdf-1.2, the salicylic acid regulated gene, PR-1, and the ethylene-response gene, HEL, also were up-regulated in plants colonized by P. chlororaphis O6, but differed in their responsiveness to drought stress. These data show how gene expression in plants lacking adequate water can be remarkably influenced by microbial colonization leading to plant protection, and the activation of the plant defense signal pathway induced by root colonization of P. chlororaphis O6 might be a key element for induced systemic tolerance by microbes.

• Biomedical Science Letters
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• v.15 no.1
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• pp.97-99
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• 2009

Geldanamycin is a benzoquinone ansamycin antibiotic that binds to cytosol HSP90 (Heat Shock Protein 90) and changes its biological function. HSP90 is involved in the intracellular important roles for the regulation of the cell cycle, cell growth, cell survival, apoptosis, angiogenesis and oncogenesis. To identify genes expressed during geldanamycin treatment against neurons of rats (PC12 cells), DNA microarray method was used. We have isolated 2 gene groups (up-or down-regulated genes) which are geldanamycin differentially expressed in neurons. Granzyme B is the gene most significantly increased among 204 up-regulated genes (more than 2 fold over-expression) and Chemokine (C-C motif) ligand 20 is the gene most dramatically decreased among 491 down-regulated genes (more than 2 fold down-expression). The gene increased expression of Cxc110, Cyp11a1, Gadd45a, Gja1, Gpx2, Ifua4, Inpp5e, Sox4, and Stip1 are involved stress-response gene, and Cryab, Dnaja1, Hspa1a, Hspa8, Hspca, Hspcb, Hspd1, Hspd1, and Hsph1 are strongly associated with protein folding. Cell cycle associated genes (Bc13, Brca2, Ccnf, Cdk2, Ddit3, Dusp6, E2f1, Illa, and Junb) and inflammatory response associated genes (Cc12, Cc120, Cxc12, Il23a, Nos2, Nppb, Tgfb1, Tlr2, and Tnt) are down-regulated more than 2 times by geldanamycin treatment. We found that geldanamycin is related to expression of many genes associated with stress response, protein folding, cell cycle, and inflammation by DNA microarray analysis. Further experimental molecular studies will be needed to figure out the exact biological function of various genes described above and the physiological change of neuronal cells by geldanamycin. The resulting data will give the one of the good clues for understanding of geldanamycin under molecular level in the neurons.