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Viruses as Nanomaterials
Published in Devarajan Thangadurai, Saher Islam, Charles Oluwaseun Adetunji, Viral and Antiviral Nanomaterials, 2022
Dushyant R. Dudhagara, Megha S. Gadhvi, Anjana K. Vala
As mentioned above, plant viruses can be used as building blocks for synthesis of nanomaterials. The natural properties of CPMV make it an attractive nanoscale building block for medical and material science applications. Generally, CPMV has a 28 nm diameter and an icosahedral capsid that contains 5.9 and 3.5 kb of positive-sense genetic material, as RNA1 and RNA2, respectively. These RNAs have a single open reading frame and are expressed through the synthesis and successive processing of precursor polyproteins. A cofactor of proteinase, 24 K proteinase, helicase, and RNA-dependent RNA polymerase are mostly found in RNA-1. RNA-2 codes for cell-to-cell and long-distance movement proteins are found in plants, as well as large (L) and small (S) coat proteins. The two domains of the L-coat protein connect with the S-coat protein, which forms asymmetric units. These 60 asymmetrical units are in control of forming the CPMV capsid (Sainsbury et al. 2010). The surface of CPMV particles is exposed and produces addressable amines (lysine), carboxylates (aspartic acid and glutamic acid), and hydroxyl (tyrosine) groups of amino acids, which can be used for various applications in selectively connected elements like redox-active molecules, fluorescent dyes, metallic and semi-conducting nanoparticles, carbohydrates, DNA, proteins, and antibodies (Steinmetz et al. 2009b).
Order Piccovirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Figure 9.2 presents some examples of the Parvoviridae genomes, according to the current ICTV report (Cotmore et al. 2019). They are linear nonpermuted ssDNA molecules of 4–6 kb in which a long coding region is bracketed by short, 116 to ~550 nucleotide, imperfect palindromes that fold into dynamic hairpin telomeres. The viruses possess two major gene cassettes; a nonstructural replication initiator gene (NS) located in the 3′ (by convention the “left”) half of the negative-sense strand and a single capsid sequence (VP) located in the right half. Most genomes also encode a small number of ancillary proteins in alternate and/or overlapping open reading frames, which are not shown in the simplified Figure 9.2. Some parvoviruses preferentially excise and encapsidate ssDNA of negative polarity, e.g. minute virus of mice (MVM) of the Protoparvovirus genus, while others encapsidate strands of either polarity in equivalent—e.g. adeno-associated virus 2 (AAV2) of the Dependoparvovirus genus—or different proportions, e.g. bovine parvovirus 1 (BPaV1) of the Bocaparvovirus genus (Cotmore et al. 2019).
Biosynthesis and Genetics of Lipopolysaccharide Core
Published in Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison, Endotoxin in Health and Disease, 2020
David E. Heinrichs, Chris Whitfield, Miguel A. Valvano
A WaaK homolog has been identified in N. meningitidis, where it is involved in the production of LOS (110). The deduced amino acid sequence of this protein shows 21% identity and 47% total similarity to the WaaK protein of Salmonella. However, the neisserial WaaK homolog shows very little similarity to the E. coli K-12 WaaU protein. Unfortunately, it is currently not known whether the neisserial waaK gene is capable of complementing either the waaK phenotype of Salmonella or the waaU phenotype of E. coli K-12. Sequence from the H. influenzae genome project (accession numbers U32734 and L42023) revealed an open reading frame whose deduced amino acid sequence indicates similarity, albeit over a small region, to the WaaU protein of E. coli K-12. Whether this open reading frame codes for a protein, and what its possible substrates are are unknown at this time.
Perspective: diagnostic laboratories should urgently develop T cell assays for SARS-CoV-2 infection
Published in Expert Review of Clinical Immunology, 2021
Rohan Ameratunga, See-Tarn Woon, Anthony Jordan, Hilary Longhurst, Euphemia Leung, Richard Steele, Klaus Lehnert, Russell Snell, Anna E. S Brooks
Responses to the S glycoprotein may reflect cross-reactive T cell responses to HCoV and increase background proliferation [49]. In the event, there are overlapping responses between HCoV and SARS-CoV-2 during clinical validation of the assay, the relevant antigens could be altered (Figure 1) [59,72,73]. Proteins and peptides derived from other open reading frames (ORFs) could be used [62]. The N or M proteins or peptides might confer greater specificity for SARS-CoV-2 [62]. Furthermore, the large dynamic range of 3H thymidine uptake assays is likely to provide clear separation of background HCoV responses to those of SARS-CoV-2. A negative response most likely indicates absence of exposure to the virus. The possibility of immunodeficiency will be excluded by normal response to lectins and other antigens.
Exosomal biomarkers for cancer diagnosis and patient monitoring
Published in Expert Review of Molecular Diagnostics, 2020
Recently, a bioinformatics analysis identified several potential exosomal targets for pancreatic cancer diagnosis [15]. The study incorporated meta-analysis tools such as GeneCards, variant analyses, and pathway mapping to identify these putative leads. The study identified 575 protein-coding genes, 26 miRNAs, one pseudogene, one long non-coding RNA, and one antisense gene directly associated with pancreatic cancer. Some of the miRNAs identified in this analysis such as miR-21, miR-34a, miR-155, miR-210, and miR-221 have previously been described as causally linked to pancreatic cancer progression [15]. Additionally, nine open reading frames were identified. Many of these targets were readily identified in exosomes found in blood, plasma, saliva, and serum, which marks them as having strong diagnostic potential. This study provides a framework with which to develop a potentially new diagnostic, and as such, further work is required to test the efficacy of the predictions laid out in this study [15].
Nicotinamide nucleotide transhydrogenase expression analysis in multiple sclerosis patients
Published in International Journal of Neuroscience, 2019
Mohammad Mahdi Eftekharian, Mohammad Taheri, Shahram Arsang-Jang, Alireza Komaki, Soudeh Ghafouri-Fard
Nicotinamide nucleotide transhydrogenase (NNT) is a mitochondrial redox-induced proton pump that links NADPH synthesis to the mitochondrial metabolic pathway. Over-expression of NNT transcripts in immune associated tissues especially in the process of macrophage activation have indicated its role in the regulation of the immune response and host protection mechanisms against pathogenic microorganisms [1]. The presence of macrophages in demyelinating lesions of multiple sclerosis (MS) patients in association with the amount of myelin loss [2] suggest participation of these immune cells in the pathogenesis of MS. Beside, deficiency of NNT from mitochondria has resulted in induction of expression of uncoupling protein 2 (UCP2) [3] another protein with a role in macrophage-mediated immune response [4]. The genomic locus of NNT contains another gene with no open reading frame for translation to protein. Based on its position relative to NNT, it has been called NNT-antisense 1 (NNT-AS1). This long non-coding RNA (lncRNA) has been shown to exert anti-proliferative effects in some tissues [5]. However, the role of this lncRNA has not been explored in the pathogenesis of immune-related disorders.