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Dua, Pooja,Ren, Shuo,Lee, Sang Wook,Kim, Joon-Ki,Shin, Hye-su,Jeong, OK-Chan,Kim, Soyoun,Lee, Dong-Ki Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.11
Escherichia coli are important indicator organisms, used routinely for the monitoring of water and food safety. For quick, sensitive and real-time detection of E. coli we developed a 2'F modified RNA aptamer Ec3, by Cell-SELEX. The 31 nucleotide truncated Ec3 demonstrated improved binding and low nano-molar affinity to E. coli. The aptamer developed by us out-performs the commercial antibody and aptamer used for E. coli detection. Ec3(31) aptamer based E. coli detection was done using three different detection formats and the assay sensitivities were determined. Conventional Ec3(31)-biotin-streptavidin magnetic separation could detect E. coli with a limit of detection of $1.3{\times}10^6CFU/ml$. Although, optical analytic technique, biolayer interferometry, did not improve the sensitivity of detection for whole cells, a very significant improvement in the detection was seen with the E. coli cell lysate ($5{\times}10^4CFU/ml$). Finally we developed Electrochemical Impedance Spectroscopy (EIS) gap capacitance biosensor that has detection limits of $2{\times}10^4CFU/mL$ of E. coli cells, without any labeling and signal amplification techniques. We believe that our developed method can step towards more complex and real sample application.
Evaluation of Toxicity and Gene Expression Changes Triggered by Oxide Nanoparticles
Dua, Pooja,Chaudhari, Kiran N.,Lee, Chang-Han,Chaudhari, Nitin K.,Hong, Sun-Woo,Yu, Jong-Sung,Kim, So-Youn,Lee, Dong-Ki Korean Chemical Society 2011 Bulletin of the Korean Chemical Society Vol.32 No.6
Several studies have demonstrated that nanoparticles (NPs) have toxic effects on cultured cell lines, yet there are no clear data describing the overall molecular changes induced by NPs currently in use for human applications. In this study, the in vitro cytotoxicity of three oxide NPs of around 100 nm size, namely, mesoporous silica (MCM-41), iron oxide ($Fe_2O_3$-NPs), and zinc oxide (ZnO-NPs), was evaluated in the human embryonic kidney cell line HEK293. Cell viability assays demonstrated that 100 ${\mu}g/mL$ MCM-41, 100 ${\mu}g/mL$ $Fe_2O_3$, and 12.5 ${\mu}g/mL$ ZnO exhibited 20% reductions in HEK293 cell viability in 24 hrs. DNA microarray analysis was performed on cells treated with these oxide NPs and further validated by real time PCR to understand cytotoxic changes occurring at the molecular level. Microarray analysis of NP-treated cells identified a number of up- and down-regulated genes that were found to be associated with inflammation, stress, and the cell death and defense response. At both the cellular and molecular levels, the toxicity was observed in the following order: ZnO-NPs > $Fe_2O_3$-NPs > MCM-41. In conclusion, our study provides important information regarding the toxicity of these three commonly used oxide NPs, which should be useful in future biomedical applications of these nanoparticles.
Evaluation of Toxicity and Gene Expression Changes Triggered by Quantum Dots
Dua, Pooja,Jeong, So-Hee,Lee, Shi-Eun,Hong, Sun-Woo,Kim, So-Youn,Lee, Dong-Ki Korean Chemical Society 2010 Bulletin of the Korean Chemical Society Vol.31 No.6
Quantum dots (QDs) are extensively employed for biomedical research as a fluorescence reporter and their use for various labeling applications will continue to increase as they are preferred over conventional labeling methods for various reasons. However, concerns have been raised over the toxicity of these particles in the biological system. Till date no thorough investigation has been carried out to identify the molecular signatures of QD mediated toxicity. In this study we evaluated the toxicity of CdSe, $Cd_{1-x}Zn_xS$/ZnS and CdSe/ZnS quantum dots having different spectral properties (red, blue, green) using human embryonic kidney fibroblast cells (HEK293). Cell viability assay for both short and long duration exposure show concentration material dependent toxicity, in the order of CdSe > $Cd_{1-x}Zn_xS$/ZnS > CdSe/ZnS. Genome wide changes in the expression of genes upon QD exposure was also analyzed by wholegenome microarray. All the three QDs show increase in the expression of genes related to apoptosis, inflammation and response towards stress and wounding. Further comparison of coated versus uncoated CdSe QD-mediated cell death and molecular changes suggests that ZnS coating could reduce QD mediated cytotoxicity to some extent only.
Evaluation of Toxicity and Gene Expression Changes Triggered by Oxide Nanoparticles
Pooja Dua,김소연,유종성,홍선우,Nitin K. Chaudhari,Chang Han Lee,chaudhari kiran nanaji,Dong-ki Lee 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.6
Several studies have demonstrated that nanoparticles (NPs) have toxic effects on cultured cell lines, yet there are no clear data describing the overall molecular changes induced by NPs currently in use for human applications. In this study, the in vitro cytotoxicity of three oxide NPs of around 100 nm size, namely,mesoporous silica (MCM-41), iron oxide (Fe_2O_3-NPs), and zinc oxide (ZnO-NPs), was evaluated in the human embryonic kidney cell line HEK293. Cell viability assays demonstrated that 100 μg/mL MCM-41, 100 μg/mL Fe_2O_3, and 12.5 μg/mL ZnO exhibited 20% reductions in HEK293 cell viability in 24 hrs. DNA microarray analysis was performed on cells treated with these oxide NPs and further validated by real time PCR to understand cytotoxic changes occurring at the molecular level. Microarray analysis of NP-treated cells identified a number of up- and down-regulated genes that were found to be associated with inflammation,stress, and the cell death and defense response. At both the cellular and molecular levels, the toxicity was observed in the following order: ZnO-NPs > Fe_2O_3-NPs > MCM-41. In conclusion, our study provides important information regarding the toxicity of these three commonly used oxide NPs, which should be useful in future biomedical applications of these nanoparticles
Dong-ki Lee,Pooja Dua,Shuo Ren,Sang Wook Lee,김준기,Hye-su Shin,정옥찬,Soyoun Kim 한국분자세포생물학회 2016 Molecules and cells Vol.39 No.11
Escherichia coli are important indicator organisms, used routinely for the monitoring of water and food safety. For quick, sensitive and real-time detection of E. coli we de-veloped a 2F modified RNA aptamer Ec3, by Cell-SELEX. The 31 nucleotide truncated Ec3 demonstrated improved binding and low nano-molar affinity to E. coli. The ap-tamer developed by us out-performs the commercial antibody and aptamer used for E. coli detection. Ec3(31) aptamer based E. coli detection was done using three different detection formats and the assay sensitivities were determined. Conventional Ec3(31)-biotin-streptavidin magnetic separation could detect E. coli with a limit of detection of 1.3 106 CFU/ml. Although, optical analytic technique, bio-layer interferometry, did not improve the sensitivity of detection for whole cells, a very significant improvement in the detection was seen with the E. coli cell lysate (5 104 CFU/ml). Finally we developed Electrochemical Impedance Spectroscopy (EIS) gap capacitance biosensor that has detection limits of 2 104 CFU/mL of E. coli cells, without any labeling and signal amplification techniques. We believe that our developed method can step towards more complex and real sample application.
Selection of DNA Aptamers Against Botulinum Neurotoxin E for Development of Fluorescent Aptasensor
Shuo Ren,신혜수,Vinayakumar Gedi,Pooja Dua,이동기,김소연 대한화학회 2017 Bulletin of the Korean Chemical Society Vol.38 No.3
Botulinum neurotoxins (BoNTs) produced by Clostridium botulinum are the deadliest toxins known to mankind with a potential of possible bioterrorism agents. Due to the high-potential harm of these toxins, a sensitive and real-time monitoring capable detection systems are required for the early stage detection. In this study, a novel sol–gel-based SELEX was used to isolate single-stranded nucleic acids (ssDNA) aptamers against purified BoNT type E toxoid (BoNTE) using a chemically synthesized random N40 ssDNA library. The bound aptamer sequences after five rounds were analyzed using next-generation sequencing and the resulted high-frequency aptamers were characterized using biolayer interferometry. Among the tested, aptamer BT5.6 showed low nanomolar binding affinity (KD, 53.3 nM) toward BoNTE. As a proof of concept, the aptamer was utilized in a graphene oxide-based detection platform. In summary, we screened and identified a ssDNA aptamer with high affinity toward BoNTE, which, we believe can be used for development of sensitive detection systems.