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Genome Editing Tools
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Madhumita Barooah, Dibya Jyoti Hazarika
TALEN (transcription activator-like effector nuclease) is an excellent tool for the manipulation of genes through site-directed mutagenesis (Sun and Zhao, 2013). TALENs employ TAL proteins for DNA binding. These proteins are derived originally from a plant pathogenic bacterial genus Xanthomonas. The DNA-binding effectiveness of TAL proteins are so high that they can recognize even very short sequences for binding, i.e., 1–2 nucleotides. Furthermore, these nucleases consist of 34-amino-acid tandem repeats that ensure their binding to the target site (Juillerat et al., 2014; Jaiswal et al., 2019). Gene knock-in (HDR) and gene knockout (NHEJ) can be performed using TALENs. This system contains two protein domains, one of which recognizes and binds the very unique and specific target site and the second one is used for cleavage of a specific sequence at that unique site (Jaiswal et al., 2019). However, this technique is applied to manipulate the genomes of many eukaryotic targets such as mammalian cells, frog, zebrafish, mouse, rat, and chicken (Lei et al., 2012; Moore et al., 2012; Bloom et al., 2013; Qiu et al., 2013; Park et al., 2014; Chen et al., 2017).
Regulating Gene-Edited Products in Nigeria
Published in Sylvia Uzochukwu, Nwadiuto (Diuto) Esiobu, Arinze Stanley Okoli, Emeka Godfrey Nwoba, Christpeace Nwagbo Ezebuiro, Charles Oluwaseun Adetunji, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Biosafety and Bioethics in Biotechnology, 2022
Gene-editing techniques are categorized into site-directed nuclease (SDN)-1, SDN-2, and SDN-3. SDN-1 involves the unguided repair of a targeted double-strand break (DSB) by the mechanism called non-homologous end joining. The spontaneous repair of this break can lead to a mutation causing gene silencing, gene knock-out or a change in the activity of a gene. SDN-2 involves a template-guided repair of a targeted DSB using a sequence donor, typically short single-stranded DNA. The donor carries one or several small mutations flanked by two sequences matching both ends of the DSB, and is thus recognized as a repair template, allowing the introduction of the mutation(s) at the target site. SDN-3 involves a template-guided repair of a targeted DSB using a sequence donor, typically double-stranded DNA containing an entire gene or an even longer genetic element. Both ends of the donor are homologous to the DSB ends, which therefore recognize the donor as a repair template, allowing the introduction of the gene or genetic element(s) at the target site (Ricroch, 2019; Friedrichs et al., 2019a). Examples of plants in which gene-editing studies are being carried out include barley, maize, wheat, soybean, sorghum and rice (Waquar et al., 2020).
Structure of networks
Published in Karthik Raman, An Introduction to Computational Systems Biology, 2021
The classic perturbation study in molecular biology is a ‘gene knock-out’ study, where a particular gene is knocked out (or silenced), and the phenotype of the organism is studied. The in silico equivalent of that would be to remove a node from the network, along with all its edges. Another very interesting perturbation is that of removing specific edges in a network, known as edgetic (from edge-specific genetic; see also §4.2.3) perturbations. Biologically, this would mean disrupting specific molecular interactions, e.g. protein–protein interactions, without removing the protein itself. This is far more challenging, although a recent study in 2018 has shown how it is indeed possible to selectively target a specific domain in a protein [47], essentially achieving a selective modulation of intracellular signalling. Vidal and co-workers developed a methodology to use ‘edgetic’ alleles that lacked single interactions, while retaining all others (see §4.2.3).
HPLC-DAD profiling and inhibitory potentials of ethylacetate and aqueous extracts of Talinum triangulare on key enzymes linked to type-2 diabetes (α-amylase and α-glucosidase) and oxidative stress (monoamine oxidase)
Published in Egyptian Journal of Basic and Applied Sciences, 2019
Olakunle B. Afolabi, Omotade I. Oloyede, Oludare S. Agunbiade, Tajudeen O. Obafemi, B. Aline, A. Obajuluwa, K. Jaiyesimi, S. Anadozie
Recently, it has been shown that, the catalytic activities of biologically active monoamine oxidases (MAO) in the deamination of aliphatic and aromatic amines in the parenchymatous tissues of vertebrates also contribute to the generation of free radicals [11], which has directly been connected with mitochondrial, endothelial and contractile dysfunction [12,13]. However, a large amount of ROS are often produced in the mitochondrial as a result of several mutations leading to disturbances in the respiratory chain as well as the loss of control of ROS production at the level of respiratory complexes [14]. Similarly, excessive ROS formation, increased levels of malonylaldehyde (MDA) and protein oxidation in the adipose tissues have hallmarked increased activities of MAO in the mitochondrial of a subject with insulin-specific receptor gene knock-out, signaling mitochondrial dysfunction [15].
Zearalenone perturbs the circadian clock and inhibits testosterone synthesis in mouse Leydig cells
Published in Journal of Toxicology and Environmental Health, Part A, 2021
Lijia Zhao, Yaoyao Xiao, Cuimei Li, Jing Zhang, Yaojia Zhang, Meina Wu, Tiantian Ma, Luda Yang, Xiaoyu Wang, Haizhen Jiang, Qian Li, Hongcong Zhao, Yiqun Wang, Aihua Wang, Yaping Jin, Huatao Chen
It was postulated that ZEA might inhibit testosterone synthesis by perturbing the circadian clock in mouse LCs. We examined the effects of ZEA on PER2::LUC oscillations in mouse primary LCs isolated from PER2::LUCIFERASE reporter gene knock in mice. In addition the influence of ZEA was assessed on the expression profiles of several canonical clock genes and steroidogenic genes, as well as testosterone synthesis in TM3 cells and primary LCs. Further, the in vivo consequences of ZEA exposure on the expression of core clock and steroidogenic genes in testes of mice as well as serum testosterone levels were determined.
Gene drive to reduce malaria transmission in sub-Saharan Africa
Published in Journal of Responsible Innovation, 2018
Austin Burt, Mamadou Coulibaly, Andrea Crisanti, Abdoulaye Diabate, Jonathan K. Kayondo
Homing can be used for vector control in a number of different ways. Conceptually, the simplest is to use it to produce a population-wide gene knock-out (Figure 5). The effect of this on the mosquito population and on malaria transmission will then depend upon the gene being targeted.