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Toxicogenomics
Published in Frank A. Barile, Barile’s Clinical Toxicology, 2019
Anirudh J. Chintalapati, Zacharoula Konsoula, Barile Frank A.
The cDNA microarray can be applied to examine gene expression changes as indications of chemical reactions. Following treatment with chemicals (i.e., polycyclic aromatic hydrocarbons, peroxisome proliferators, or estrogenic chemicals), a gene expression “trademark” on a cDNA microarray is presented, which corresponds to the cellular or tissue chain reactions to these chemicals. The response to different chemicals precipitates changes in the expression levels of many genes, which connote a general toxic response; however, a subpopulation of the expressed genes is designated as being exclusive to a distinct class of compounds, specifically at low doses. This application signals compounds as potential carcinogens/toxicants and unfolds their mode of action by elucidating the mediated signal transduction pathways. Table 12.6 summarizes the applications of microarrays in toxicology.
Encephalitozoon
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Alexandra Valencakova, Lenka Luptakova, Monika Halanova, Olga Danisova
The report about the implementation of methods of DNA chips (DNA “microarray”) for the parallel detection of several species of microsporidia (E. cuniculi, E. hellem, and E. intestinalis) in clinical samples75 is very interesting. The great advantage of a DNA “microarray” compared to the PCR method is the ability to diagnose a high number of unknown samples. Unlike PCR, DNA is not obtained through laborious processing of spores by preextraction steps, but by using FTA filters, which not only eliminates these labor-intensive procedures, but also helps avoid the significant loss of DNA and effectively removes inhibitors from fecal samples. Compared to the commercial DNA extraction kits, this method results in lower financial costs, requires less technical training, requires less equipment, and can process a larger number of samples simultaneously.76 The disadvantage of DNA “microarray” is not only expensive laboratory instrumentation, but also the synthesis of large amounts of primers. But once the preparation of the DNA microarray is completed, the actual execution of tests is considerably cheaper. The method of the DNA microarray, as described by Wang et al. (2005),75 represents a combination of the PCR method, which is followed by hybridization of the amplicons using more specific probes immobilized on a microchip. The fluorescence intensity correlates with the abundance of DNA in a sample.
Two-Dimensional Microfluidic Bioarray for Nucleic Acid Analysis
Published in Iniewski Krzysztof, Integrated Microsystems, 2017
DNA microarray hybridization has been an important technique in genomic research. Because of their flexibility and low production cost, microarrays with low-density probes have been used in SNP detection as well as nucleic acid diagnostic applications. Recently, microfluidic technology was combined with the DNA microarray method through covering the spotted probe area with chambers or microchannels for sample hybridization. As summarized in this chapter, the microfluidic microarray method shows the advantages of less sample usage, fast reaction kinetics, as well as multiple sample capabilities for high-throughput analysis.
Overview of gene expression techniques with an emphasis on vitamin D related studies
Published in Current Medical Research and Opinion, 2023
Jeffrey Justin Margret, Sushil K. Jain
In DNA microarray analysis, an array of oligonucleotide probes bound to a chip surface enables high-throughput gene expression profiling of multiple genes18. This valuable research tool helps identify specific DNA sequences in complex nucleic acid samples. On the DNA microarray chip, labeled cDNA is hybridized to a complementary probe sequence arranged on a relatively small surface. It allows the expression of thousands of genes to be monitored simultaneously, thereby providing a functional way to sequence information across different regions of a genome19 (Figure 2). Microarrays can produce massive amounts of information requiring a series of consecutive analyses to render the data interpretable20. Genomic microarrays are used to determine the transcriptional program of the cellular function and identify genome-wide binding sites for transcriptional factors that regulate genes, gene function, and identify new therapeutic targets21. Clinical trials of various disorders frequently use this technique to study gene expression patterns and identify candidate genes. While the quality and amount of RNA required by microarray remain a major challenge, the gene information provided by this technique is extremely useful22. However, microarray is not suitable for absolute quantification, separate detection of canonical miRNAs, or identification of any novel miRNAs23.
Development of a novel anti-liver fibrosis formula with luteolin, licochalcone A, aloe-emodin and acacetin by network pharmacology and transcriptomics analysis
Published in Pharmaceutical Biology, 2021
Yuan Zhou, Rong Wu, Fei-fei Cai, Wen-Jun Zhou, Yi-Yu Lu, Hui Zhang, Qi-Long Chen, Ming-Yu Sun, Shi-Bing Su
Blood samples from chronic hepatitis B patients with or without LDSDS (n = 16 for each group) were collected. This study was approved by the Ethics Committee of Shanghai University of Traditional Chinese Medicine, and all participants provided a written informed consent form before enrolment. Cellular RNA from blood cells were purified using RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. The RNA integrity number was determined by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and then stored at −80 °C until use. For the cDNA microarray analysis, samples were labelled using Low Input Quick Amp Labelling Kit, and hybridized to the cDNA array by Gene Expression Hybridization Kit (Agilent Technologies). The arrays were scanned by Agilent Microarray Scanner (Agilent Technologies) with default settings, and the raw data were analyzed by the Feature Extraction software 10.7 (Agilent Technologies) and normalized using the Quantile algorithm and Gene Spring Software 11.0 (Agilent Technologies). The transcriptomic data of the differentially expressed genes (DEGs) were obtained after the SAS online software analysis for a fold change >1.5 and p < 0.05.
Could a blood test for PTSD and depression be on the horizon?
Published in Expert Review of Proteomics, 2018
In addition, gene-activity assay is a promising technique and cost-efficient; however, this technology requires more investigation to identify specific genes that change their expression in PTSD and MDD [88]. DNA microarrays can efficiently highlight gene expression profiling of transcriptional reactivity. Currently, studies that analyze gene expression related to PTSD showed relevant signatures in mononuclear cells that may be useful to diagnose a mental disorder [272]. However, improved methods are still required to screen more efficiently through sets of candidate variants, and then, a rigorous validation of variants and gene effects are also needed [273]. Furthermore, replications in larger samples and investigations focusing on selected markers as part of the biosignatures that have been discovered, are required to assess the diagnostic utility and pathological relevance of these methods.