Methods in molecular exercise physiology
Adam P. Sharples, James P. Morton, Henning Wackerhage in Molecular Exercise Physiology, 2022
Inherited genetic variations or epigenetic modifications, as a result of exercise, are able to effect whether a gene is turned on or off. The process of turning a gene on or off is termed gene transcription or expression (the full theory for gene transcription is described in detail in Chapter 3). In order to measure gene expression, RNA must first be isolated. As with DNA, researchers are able to directly extract RNA from skeletal muscle tissue to study gene expression following exercise. RNA is very similar to DNA; however, RNA is single-stranded, whereas DNA is double-stranded (i.e. the double helix structure); the sugar backbone in RNA is ribose compared with deoxyribose within DNA (hence why RNA is much less stable than DNA) and there is a replacement of thymine (T) in DNA with uracil (U) in RNA (see Chapter 3, Figure 3.7). Also known as mRNA, the RNA copies and delivers the DNA ‘message’ to the protein-making machinery of the cell (i.e. the ribosome) to initiate the production of protein. Therefore, as suggested above, the making or synthesis of RNA from DNA is termed transcription, whereas the synthesis of protein from transcribed mRNA is termed translation.
Basic genetics and patterns of inheritance
Hung N. Winn, Frank A. Chervenak, Roberto Romero in Clinical Maternal-Fetal Medicine Online, 2021
Genes are composed of deoxyribonucleic acid (DNA) and are contained on the chromosomes. Each strand of DNA has a specific sequence of four nucleotides, each containing a different base, adenine, thymine, cytosine, or guanine. Adenine pairs with thymine and cytosine pairs with guanine as two complementary strands of DNA are wound together to form a double helix. Genes have a common basic structure (Fig. 20). First, there are upstream sequences that regulate transcription, known as promoters and enhancers. Then, there is a transcription initiation site, followed by a series of alternating exons and introns. The DNA sequence serves as a template from which messenger RNA (mRNA) is made; this process is known as transcription. As transcription proceeds, a primary mRNA is made from the DNA sequence of the gene, which includes the introns. The intron sequences are then spliced out and the exons are linked together to form the mature mRNA molecule. Thus, the exons are the only portions of the gene that specify the final protein product. The mature mRNA molecule is used to make the protein product by the process of translation. Groups of three nucleotides, called codons, code for specific amino acids. Transfer RNA (tRNA) and ribosomal RNA (rRNA) interact with the mRNA to assemble the amino acids into a polypeptide chain to form the final protein molecule.
RNA-seq Analysis
Altuna Akalin in Computational Genomics with R, 2020
RNA sequencing (RNA-seq) has proven to be a revolutionary tool since the time it was introduced. The throughput, accuracy, and resolution of data produced with RNA-seq has been instrumental in the study of transcriptomics in the last decade (Wang et al., 2009). There is a variety of applications of transcriptome sequencing and each application may consist of different chains of tools each with many alternatives (Conesa et al., 2016). In this chapter, we are going to demonstrate a common workflow for doing differential expression analysis with downstream applications such as GO term and gene set enrichment analysis. We assume that the sequencing data was generated using one of the NGS sequencing platforms. Where applicable, we will try to provide alternatives to the reader in terms of both the tools to carry out a demonstrated analysis and also the other applications of the same sequencing data depending on the different biological questions.
Blocking SP/NK1R signaling improves spinal cord hemisection by inhibiting the release of pro-inflammatory cytokines in rabbits
Published in The Journal of Spinal Cord Medicine, 2023
Yuehuan Zheng, Nannan Wang, Zhe Chen, Liqiang Shi, Xiangyang Xu
The normal functioning of the central nervous system (CNS) requires the interaction of multiple cell types, including neurons, glial cells, and non-nerve cells.23 Electron microscopy shows that the nissl body is a ribosome similar to the rough endoplasmic reticulum pool in neurons. Each ribosome is a complex composed of rRNA and proteins that use transfer RNA and amino acids to synthesize proteins from mRNA. In other words, the nissl bodies is a major component of the neuronal protein synthesis mechanism.24 It is reported that the nissl bodies is a large basophilic mass and particle in the neuronal cell body or dendrites. When neurons are damaged, the nissl bodies dissolve and even disappear. During damage recovery, the nissl bodies appear again and reach normal levels. Therefore, nissl bodies can be used as markers of the functional state of neurons.24 In this study, we preliminarily found that the number of nissl bodies increased notably in the spinal cord tissue of the rabbits in the OB group on the 7th day, suggesting that the nissl bodies may be involved in the repair process of SCI.
Clinical pharmacology of siRNA therapeutics: current status and future prospects
Published in Expert Review of Clinical Pharmacology, 2022
Ahmed Khaled Abosalha, Jacqueline Boyajian, Waqar Ahmad, Paromita Islam, Merry Ghebretatios, Sabrina Schaly, Rahul Thareja, Karan Arora, Satya Prakash
Chemical modification acts as a significant strategy to optimize the delivery of naked siRNAs to overcome some delivery obstacles. The negatively charged phosphodiester skeleton of siRNA represents a powerful barrier to its cellular uptake through the anionic lipid bilayers of the cell membrane. Furthermore, the original structure of siRNA candidates makes them highly susceptible to degradation by endonucleases with a poor pharmacokinetic profile. Also, hazardous off-target side effects such as the unintended block of expression of other genes have been reported besides triggering the host immune response [48]. Consequently, chemically modified siRNA therapeutics can offer a high degree of cellular uptake and resistance against endonucleases in addition to minimizing the harmful off-target effects and antigenicity. Generally, both DNA and RNA are composed of nucleotides as building blocks. Nucleotides compromise a ribose or 2′-deoxyribose sugar moiety with 1′-nucleobase and 3′-phosphate groups. Four sites of chemical modifications to siRNA molecules were previously proposed, including the ribose sugar, nucleobase, phosphate link, and strand terminus [17].
Development of amplification system for point-of-care test of nucleic acid
Published in Computer Methods in Biomechanics and Biomedical Engineering, 2022
Shaolei Huang, Jiageng Wu, Haozheng Dai, Runxin Gao, Hongyu Lin, Dongxu Zhang, Shengxiang Ge
The amplification system proposed in this paper is based on the principle of PCR, so the main technical requirements should meet the temperature conditions of the three processes, which are denaturation, annealing and extension. High-temperature denaturation process needs to be carried out at the temperature of 95 °C to open the double helix structure. Detection of RNA is slightly different from DNA. The temperature condition of 50 °C needs to be added for its reverse transcription; During low temperature annealing, the primer and the single strand are combined according to the principle of base pairing, and the temperature should be maintained at 55 °C; Primer extension process requires temperature condition of 72 °C to achieve the synthesis of complementary strands, and the nucleic acid polymerase will extend along the direction of phosphate (5′-3′) (Harve et al. 2010). It has been shown that if the target nucleic acid fragment to be amplified is short (100-300 bp), a two-step PCR can be used, namely two temperature conditions where the extension phase can occur during the transition between annealing and denaturation temperatures and does not require a holding time (Wittwer and Garling 1991, Wittwer et al. 2001). Generally, the above process needs to be repeated about 40 to 50 cycles and the temperature conditions between the cycles should be consistent. In addition, to meet the requirements of POCT, it is necessary to complete at least 45 cycles of the process within 30 minutes, that is, the average temperature change velocity is not less than 4 °C/s.
Related Knowledge Centers
- DNA
- Macromolecule
- Nucleic Acid
- Nucleobase
- Nucleotide
- Polymer
- Uracil
- Messenger Rna
- Guanine
- NON-Coding Rna
- Messenger Rna
- DNA