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Bayesian Inference: Biological Processes that Follow a Continuous Time Markov Chain
Published in Lyle D. Broemeling, Bayesian Analysis of Infectious Diseases, 2021
This model makes a distinction between transitions and transversions, which distinguishes between the substitutions a ↔ g (from purine to purine) or from pyrimidine to pyrimidine, and transversions, from purine to pyrimidine or vice versa, that is, the substitutions c ↔ t .
Lung Cancer
Published in Pat Price, Karol Sikora, Treatment of Cancer, 2020
These consist of high-grade neuroendocrine tumors (HG NET) such as small-cell lung cancer (SCLC) and large cell neuroendocrine or more indolent carcinoid tumors. HG NET are usually associated with a history of heavy smoking and are typically found in the major bronchi. These tumors are frequently observed to secrete antidiuretic hormone, calcitonin, and adrenocorticotrophic hormone in either an autocrine or a paracrine manner. Macroscopically, tumors are friable with a pinky cut surface. Microscopically, SCLCs are characterized by the presence of small cells with large pleomorphic nuclei and scanty cytoplasm. The majority of SCLCs express thyroid transcription factor-1 (TTF-1) as well as neuroendocrine markers such as chromogranin, synaptophysin, and CD56. At the molecular level, G to T transversion mutations, which are characteristic of smoking, are common. SCLC tumors show a high density of somatic DNA aberrations, and allelic loss of tumor suppressor genes is commonest, with p53 and Rb being universally affected.5
Introductory Remarks
Published in Dongyou Liu, Handbook of Tumor Syndromes, 2020
Representing the most common form of small-scale mutation (with small-scale mutation involving a single nucleotide being referred to as point mutation), base substitution consists of transition and transversion. Transition involves exchange of a purine for another purine (A ↔ G) or of a pyrimidine for another pyrimidine (T ↔ C), while transversion involves exchange of a purine for a pyrimidine or of a pyrimidine for a purine (C/T ↔ A/G). Base substitution leads to synonymous codon with no amino acid change is referred to as silent mutation, base substitution that generates a codon that encodes a different amino acid is referred to as missense mutation, and base substitution results in a stop codon with a truncating translation and nonfunctional protein is referred to as nonsense mutation. Small scale mutation due to insertion of additional base pairs in the coding region of a gene may alter splicing of the mRNA (spice-site mutation) or cause a shift in the reading frame (frameshift), resulting in an altered gene product. Small scale mutation due to deletion of one or more base pairs from the coding region of a gene may also cause frameshift, and possibly a nonfunctional product. Small-scale mutation that involves gene amplification and expansion of trinucleotide repeats is known as copy number variation (e.g., congenital central hypoventilation syndrome [CCHS], see Chapter 4) [4].
Insights and controversies on sunscreen safety
Published in Critical Reviews in Toxicology, 2020
Juliana P. Paiva, Raiane R. Diniz, Alvaro C. Leitão, Lucio M. Cabral, Rodrigo S. Fortunato, Bianca A. M. C. Santos, Marcelo de Pádula
In addition, both UVA and UVB radiations participate in oxidative processes at cellular and molecular levels in different proportions (Schuch et al. 2017). One of the most frequent ROS-induced modifications in DNA is 8-hydroxy-2′-deoxyguanosine (8-OHdG) (Douki et al. 2003; Wondrak et al. 2006) due to the low redox potential of guanine when compared to the other DNA bases (Hickerson et al. 1999; Margolin et al. 2006). Although aerobic respiration can lead to spontaneous production of 8-OHdG, this pre-mutagenic lesion can also be induced by UV-exposure (Wamer et al. 1997). Mutagenesis may occur because the progression of DNA replication occurring on existing damaged bases sites, leading to GC to TA transversions originating from replication events on 8-OHdG as result of an erroneous pairing with adenine (Thomas et al. 1997; Neeley and Essigmann 2006; Shockley et al. 2013). In general, 8-OHdG generation in DNA involves the attack of 1O2 and •OH, resulting from both types II and I photosensitization reactions during UV exposure (Pouget et al. 2000; Cadet et al. 2009). In addition, 8-OHdG may be formed by DNA direct irradiation with 1O2 generation since DNA molecule itself acts as a chromophore for UVA light (Yagura et al. 2017). The accumulation of the cited lesions in unrepaired DNA increases the frequency of mutation, contributing to the development of carcinogenic process.
Hepatitis E virus isolated from chronic hepatitis B patients in Malaysia: Sequences analysis and genetic diversity suggest zoonotic origin
Published in Alexandria Journal of Medicine, 2018
Shuaibu Abdullahi Hudu, Mohd Taib Niazlin, Syafinaz Amin Nordin, Nabil Saad Harmal, Soek Siam Tan, Haniza Omar, Hamiza Shahar, Noor Aliza Mutalib, Zamberi Sekawi
This evolutionary relationship was computed using the Kimura 2-parameter model with gamma distribution. Further bioinformatics analysis revealed that nucleotide substitution as well as transversion rates showed that transition and transversion occurred most with cytosine and thymine (25.11%), followed by substitutions between thymine and guanine (19.34%). Amino acid sequence analysis of our isolates compared to a reference swine HEV from China which exhibited 99% similarity with our sequences showed that our isolates had 3 to 11 amino acid variations from the swine HEV at different positions of the gene. However, all the Malaysian isolates shared an amino acid difference at position 22 of the ORF-2 gene where phenylalanine (F) in swine HEV was replaced by leucine (L) in human HEV (Fig. 4a). On the other hand, when compared with the Indian isolate with the lowest sequence similarity (89.3%), our Malaysian isolates showed more variations in amino acids than the China swine isolates but shared an amino acid variation at six different positions: D37G, S78P, T124V, A574T, V620A and T625V. The lowest number of amino acid differences from this Indian isolate was found in the Malaysian isolate KX426582, which differed from the Indian swine isolate by only 11 amino acids (Fig. 4b).
TP53 codon 72 polymorphism and the risk of glaucoma in a north Indian cohort: A genetic association study
Published in Ophthalmic Genetics, 2018
Shashank Gupta, Souradip Chatterjee, Abhishek Chandra, Om Prakash Singh Maurya, Ravindra Nath Mishra, Ashim Mukherjee, Mousumi Mutsuddi
If we consider the genotypic distributions in the present study, it is notable that the Pro-Arg heterozygotes constitute the majority of the healthy population (nearly 54% in controls, Table 2). Moreover, the Pro allele appears to be protective and thus the Pro homozygotes are higher in controls. As far as either of the Pro alleles undergoes transversion as in heterozygotes, there appears to be no major health problem. However, when both the Pro alleles are mutated to Arg, it imposes a significant disease risk. In other populations, the contrary should be true, where the Arg allele is protective and the Pro homozygosity confers the disease risk. Interestingly, most of the studies indicating the association of this SNP with glaucoma find the risk associated either with the Pro or with the Arg homozygotes. Therefore, we predict that it is the distribution of the Pro or Arg homozygotes rather than the heterozygotes that is important in the examined population to decide the disease status. In addition, there can also be involvement of some unidentified factors, which, in combination with Pro or the Arg homozygosity, influence the predisposition toward glaucoma.