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The Viruses
Published in Julius P. Kreier, Infection, Resistance, and Immunity, 2022
Poliovirus has a relatively simple method of replication. The virus enters susceptible cells following attachment to cellular receptors, new virus production occurs within the cytoplasm, and cells are lysed to release the progeny virions. The single-stranded RNA genome is plus-stranded, as is cellular messenger RNA. This enables the viral RNA to be translated directly after uncoating. The result of translation is a single large protein which is cleaved into an RNA-dependent RNA polymerase, and also into four polypeptides that form the individual capsomers of the nucleocapsid. The genomic RNA is copied by the viral polymerase into a complementary strand of RNA that serves as the replicative form of the virus. New virions assemble in the cytoplasm within inclusion bodies and are released following cytolysis.
SARS-CoV-2 and Its Variants
Published in Srijan Goswami, Chiranjeeb Dey, COVID-19 and SARS-CoV-2, 2022
Srijan Goswami, Ushmita Gupta Bakshi, Shreya Bhattacharya
In Chapter 2, the author described the morphology, genomic organization, and life cycle of the original SARS-CoV-2 in detail. In this section, the authors provide a quick and brief overview of the replication and life cycle of the original SARS-CoV-2, which is necessary to understand the context of the present chapter. SARS-CoV-2 possesses an important structure called the spike (S) protein on its outer covering made of a phospholipid bilayer. Inside the virus, there is positive-sense single-stranded RNA as genetic material. These two components are vital in relation to the formation of variants.
Evolution
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Finally, to solve once and for all the problem of the inactive double-stranded RNAs, Usui et al. (2015) introduced 28 various predicted structures into the MDV-1 vector. As a result, a simple rule regarding the single-stranded RNA genome was extracted, namely, replication with less double-stranded RNA formation or less GC number in loops. Then, the authors designed an artificial RNA that encoded the α domain of the β-galactosidase gene based on this rule. Moreover, the evidence was obtained that this rule governed the natural genomes of all bacterial and most fungal viruses presently known. Therefore, this study revealed one of the structural design principles of a single-stranded RNA genome that replicated continuously with less double-stranded RNA formation (Usui et al. 2015).
Regulatory roles of extracellular vesicles in adverse pregnancy outcomes exposed with environmental toxicants
Published in Critical Reviews in Toxicology, 2022
Xiaoqing Wang, Shukun Wan, Chenyang Mi, Wenxin Huang, Rong Wang, Huidong Zhang
miRNAs are a class of non-coding single-stranded RNA molecules. miRNAs could bind with the complementary sequences (i.e. miRNA binding site) in their target mRNAs, resulting in mRNA translation inhibition or mRNA degradation (Rupaimoole and Slack 2017). miRNAs are widely present in serum or other body fluids. Secreted miRNAs, particularly from EVs, can potently and fundamentally alter the transcriptome and gene expression of the recipient cells. Moreover, EV-derived miRNAs can also mediate paracrine and endocrine communications between tissues and distal cells (Mori et al. 2019). Tumor-derived EV miRNAs might be received by neighboring or distant cells, and thus interfere with tumor immunity and microenvironment, facilitating tumor proliferation, invasion, metastasis, vascularization, and drug resistance (Sun et al. 2018). Likewise, EV-derived miRNAs also play essential roles in mediating communications between maternal uterus and blastocysts in every stage of pregnancy. In this section, we review the effects of EV-derived miRNAs on normal pregnancy and APOs, including PE and GDM.
Molecular detections of coronavirus: current and emerging methodologies
Published in Expert Review of Anti-infective Therapy, 2022
Mingkun Diao, Lang Lang, Juan Feng, Rongsong Li
Nucleic acid sequence based analysis allows precise detection of pathogens. The coronavirus genome is composed of single-stranded RNA. Hence, most of its molecular diagnostic methods are based on detecting its RNA sequences (Figure 1). Amplification-based detections, such as RT-PCR and LAMP, are commonly used molecular diagnostic methods. There are also amplification independent methods, for example, biosensor-based methods that convert the interactions of biological molecules into physical, chemical, or optical signals [7,8]. The Clustered Regularly Interspaced Short Palindromic Repeats/Clustered Regularly Interspaced Short Palindromic Repeats-associated protein (CRISPR/Cas) based methods combine amplification and the cleavage of fluorescence probe containing viral specific sequence. Whole genome sequencing can also be used for the detection of coronaviruses, but it is mostly for research purpose rather than clinic diagnostics.
Prediction of RNA secondary structure based on stem region replacement using the RSRNA algorithm
Published in Computer Methods in Biomechanics and Biomedical Engineering, 2021
Chengzhen Xu, Longjian Gao, Jin Li, Longfeng Shen, Hong Liang, Kuan Luan, Xiaomin Wu
In this study, 43 secondary structures of single-stranded RNA were extracted from the PDB and NDB databases by removing sequences that were similar or the same. Figure 1 shows a flow chart that represents the proposed algorithm. To measure the prediction accuracy, measures of sensitivity and specificity were used. According to the definition given by Baldi et al. (2000), the sensitivity and the specificity can be determined using Equation (14): SS and SP represented the sensitivity and the specificity, respectively. TP was the number of matched bases that were correctly predicted, while TN (true negative) was the number of unmatched bases that were correctly predicted. FN (false negative) was the number of existing matched bases that were not identified and FP was the number of matched bases that were incorrectly predicted. In addition, (TP+FP) was the total number of matched bases, while EP was the expected number of matched bases, and ES was the expected number of stems. Here, only secondary structure matches were considered.