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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.
Nucleic acid aptamers targeting cell-surface proteins
Dua, P.,Kim, S.,Lee, D.k. Academic Press 2011 Methods Vol.54 No.2
Aptamers are chemical antibodies that bind to their targets with high affinity and specificity. These short stretches of nucleic acids are identified using a repetitive in vitro selection and partitioning technology called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since the emergence of this technology, many modifications and variations have been introduced to enable the selection of specific ligands, even for implausible targets. For membrane protein, the selection scheme can be chosen depending upon the availability of the system, the protein characteristics and the application required. Aptamers have been generated for a significant number of disease-associated membrane proteins and have been shown to have considerable diagnostic and therapeutic importance. In this article, we review the SELEX process used for identification of aptamers that target cell-surface proteins and recapitulate their use as therapeutic and diagnostic reagents.
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
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
CGI based syslog management system for virtual machines
Kamal Dua,Tanupriya Choudhury,Uppara Rajanikanth,Amitava Choudhury 대한공간정보학회 2020 Spatial Information Research Vol.28 No.4
Undoubtedly, logs are brain of any software system. Development, debugging and upgradation of software applications became much easier due to the logging or auditing concept in computer science field. Virtual Machines also log and timestamp every activity that take place during their runtime. Gathering system details from those lengthy log files is a hectic work for the end-user since single log file contains millennial entries of audited log data. A management system can be very helpful solution and required for the analytical scanning and the visualization of the logged data and thus providing the way to end user for the relevant information about the virtual machines running on the hypervisors. The same system can help developers to gather relevant log entries and presenting data collectively to the end user. This system not only helps in providing and presenting details but also act as an alert system to notify user fatal errors occurred during runtime. Statistical usage information or notification system can further be developed by the means of this syslog system. This paper will present how developers can build an efficient Syslog Management System on the web using the (CGI) Common Gateway Interface in the C programming language and also mentions how CGI environment can be achieved in the Apache Tomcat webserver to build dynamic web tools. Also, it provides basic idea how C can be used effectively in the CGI interface to provide better methods for obtaining and extracting relevant system data.
Ankita Dua,Jaya Malhotra,Anjali Saxena,Fazlurrahman Khan,Rup Lal 한국미생물학회 2013 The journal of microbiology Vol.51 No.5
Strain L15T, a Gram-negative, motile, orange colored bacterium was isolated from pond soil in the surrounding area of a hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain L15T belongs to the family Hyphomicrobiaceae in the order Rhizobiales. Strain L15T showed highest 16S rRNA gene sequence similarity to Devosia chinhatensis IPL18T (98.0%). Chemotaxonomic data revealed that the major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C18:1 ω7c 11-methyl,C16:0 and C18:0. The major polar lipids of strain L15T were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain L15T was 59.8%. Polyamine profile showed the presence of sym-homospermidine with traces of putrescine. Ubiquinone Q-10 was the major respiratory quinone present. Based on these data, strain L15T (=CCM 7977T =DSM 25398T) was classified as a type strain of a novel species, for which the name Devosia lucknowensis sp. nov. is proposed.