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Two-Dimensional Microfluidic Bioarray for Nucleic Acid Analysis
Published in Iniewski Krzysztof, Integrated Microsystems, 2017
Nucleic acid hybridization techniques feature the use of a probe nucleic acid molecule to detect a target nucleic acid molecule. Here, probe molecules are usually short single-stranded nucleic acids (DNA or RNA) or oligonucleotides with known sequences; whereas target molecules are prepared from polymerase chain reaction (PCR) amplification of genomic extracts. Probe-target hybridization leads to the formation of a double-stranded molecule, called duplex. The concept of DNA microarray was evolved from Southern blotting technology based on solid-phase hybridization in the early 1990s [1]. This method relies on the immobilization of the probe molecules onto the solid surface to recognize their complementary DNA target sequence by hybridization. Up to millions of features have been integrated into a standard glass slide or silicon chip by microprinting or in situ synthesis of oligonucleotides [2,3]. The relative abundance of nucleic acid sequences in the target can be measured from chip-hybridization results optically, electrochemically, or radioactively, with proper detection labels [4]. DNA microarrays have dramatically accelerated many types of investigations including gene expression profiling, comparative genomic hybridization, protein–DNA interaction study (chromatin immunoprecipitation), single-nucleotide polymorphism (SNP) detection, and nucleic acid diagnostic applications. The advances in DNA microarray technology during the last couple of years have been summarized in many books and reviews [4–8].
Current Use and Future Promise of Genetic Engineering
Published in Michael Hehenberger, Zhi Xia, Huanming Yang, Our Animal Connection, 2020
Michael Hehenberger, Zhi Xia, Huanming Yang
Transcriptomics is the study of the transcriptome, defined as the set of all RNA molecules, including mRNA, rRNA, tRNA, and other noncoding RNA produced in one or a population of cells. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are expressed at any given time. The study of transcriptomics, also referred to as gene expression profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology. The transcriptomes of stem cells and cancer cells are of particular interest: transcriptomics applied to those cells help us in the understanding of cellular differentiation and carcinogenesis.
Current Use and Future Promise of Genetic Engineering
Published in Michael Hehenberger, Zhi Xia, Our Animal Connection, 2019
Transcriptomics is the study of the transcriptome, defined as the set of all RNA molecules, including mRNA, rRNA, tRNA, and other noncoding RNA produced in one or a population of cells. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are expressed at any given time. The study of transcriptomics, also referred to as gene expression profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology. The transcriptomes of stem cells and cancer cells are of particular interest: transcriptomics applied to those cells help us in the understanding of cellular differentiation and carcinogenesis.
Sequentially automated extraction of nucleic acids with magnetophoresis in microfluidic chips
Published in Instrumentation Science & Technology, 2023
M. Kashif Siddique, Ruizhi Lee, Songjing Li, Lin Sun
The proposed method offers several potential applications in biology and medicine. One application is molecular diagnostics, where the ability to extract nucleic acids from a small sample of biological material is crucial for detecting diseases caused by viruses or bacteria. The reported approach automates the extraction and reduces the time required for analysis, making it promising for rapidly and accurately diagnosing infectious diseases. Another potential application is genetic research, where extracting high-quality nucleic acids is critical for such as gene expression profiling or next-generation sequencing. The proposed method may improve the quality and quantity of nucleic acids extracted from biological samples, enabling more reliable and informative analysis. The proposed method may improve the nucleic acid extraction efficiency, accuracy, and reproducibility in various applications, making it a valuable tool for biology, medicine, and biotechnology.
Hexavalent chromium bioremediation with insight into molecular aspect: an overview
Published in Bioremediation Journal, 2021
Sreejita Ghosh, Amrita Jasu, Rina Rani Ray
For example, Plantago ovata is known to grow in sites contaminated with Cr (VI). At Cr (VI) concentration of 1.9 mM it was found that there was a 50% reduction rate in seed germination or producing some physiological alterations like reduction in the length of shoots and roots and development of multiple roots (Kundu, Dey, and Raychaudhuri 2018). But the plant employed different strategies to survive under such heavy metal stress. At Cr (VI) concentration of upto 1.5 mM, the plant produces increased amount of secondary metabolites like polyphenols, chlorophyll (chlorophyll a, b and total chlorophyll), carotenoids leading to elevated anti-oxidant activity (Kundu, Dey, and Raychaudhuri 2018). On the other hand, DPPH radical scavenging and malondialdehyde content were not increased indicating that lipid peroxidation rate was low under Cr (VI) toxicity. Phenylammonia lyase (PAL) and polyphenol oxidase (PPO) levels were increased on being exposed to Cr (VI). Atomic absorption spectroscopy revealed bioaccumulation of Cr (VI) within the roots and shoots of the plant. Gene expression profiling revealed the activity of abscisic acid, ethylene, jasmonic acid and gibberellic acid (GA) due to Cr (VI) stress (Trinh et al. 2014).
Evaluation of seeds ethanolic extracts of Triplaris gardneriana Wedd. using in vitro and in vivo toxicological methods
Published in Journal of Toxicology and Environmental Health, Part A, 2020
Thiago S. Almeida, Mariana R. Arantes, José J. Lopes Neto, Terezinha M. Souza, Igor P. Pessoa, Jackeline L. Medeiros, Pedro M. S. Tabosa, Thais B. Moreira, Davi F. Farias, Ana F. U. Carvalho
MCF7 cells were exposed to 100 μg/ml EETg, 100 µg/ml caffeic acid, 20 µg/ml gallic acid, and 40 µg/ml for quercetin, for 6 hr. RNA was isolated and subjected to RNAseq for gene expression profiling. After normalization of gene expression data, differentially expressed genes were selected, i.e. genes up- or downregulated 1.5 fold or more (2 log ratio ≥ |0.6|) in at least 3 of the samples analyzed. A heatmap of these genes is illustrated in Figure 4. The large number of genes altered by quercetin makes it difficult to see the profile of the other compounds, such that a heatmap was constructed without quercetin (Figure 5). Exposure of MCF7 cells to the EETg extract resulted in differential expression of 14 genes, 4 of these genes being up-regulated (HSPA8, SQLE, SLC3A2, SLC7A5, TFRC) and 9 down-regulated (IFIT1, MX1, OAS1, PARP10, PARP9, DDX60, ID3, PARP14, STAT1). Quercetin was the substance that induced the greatest number of gene alterations, an amount of 4,425 genes. Gallic acid was able to change the expression of 3 genes and caffeic acid altered 54 genes.