Toxicogenomics
Frank A. Barile in Barile’s Clinical Toxicology, 2019
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.
Impact of Integrated Omics Technologies for Identification of Key Genes and Enhanced Artemisinin Production in Artemisia annua L.
Tariq Aftab, M. Naeem, M. Masroor, A. Khan in Artemisia annua, 2017
Genomics is the systematic study of an organism’s genome with the help of molecular tools. Traditionally, genes have been analyzed individually, but microarray technology has advanced substantially in recent years. Various steps of genome analysis involve (1) genome sequencing, (2) identification of repetitive as well as unique sequences, (3) gene prediction, (4) identification of functional expressed sequence tags (ESTs) and complementary DNA (cDNA) sequences, and (5) genome annotation and gene location/gene mapping. Recently, DNA microarray techniques have evolved as a powerful tool, which has the potential to measure differences in DNA sequences between individuals and the expression of thousands of genes simultaneously.
Encephalitozoon
Dongyou Liu in Handbook of Foodborne Diseases, 2018
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.
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.
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.
Gene expression profiling of rat livers after continuous whole-body exposure to low-dose rate of gamma rays
Published in International Journal of Radiation Biology, 2018
To validate the cDNA microarray results on expression level for pooling samples, the expression levels of some genes were tested with real-time PCR. Figure 3 shows relative mRNA expression pattern of 15 genes. The genes with dark color (Btg2, Gadd45a, Jun, Plk2, Mir27b, Agpat9, Myh1, Hells, Hes1, and Agpat3) were shown to be up-regulated, and the genes with light color (Mir93, G6pd, Pgd, Rgs16, and Ifit1) were down-regulated in array results. The results of array and real-time PCR were similar showing that the array results are meaningful.
Related Knowledge Centers
- Biochip
- Complementary DNA
- DNA
- Fluorophore
- Gene Expression
- Genotyping
- Microarray
- Oligonucleotide
- Hybridization Probe
- Gene