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Mitochondrial DNAs and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Estimates of Neμ and Nfμ (Table 2) have been collated for a number of species. In some cases (*) 4Neμ has been estimated from data on allozyme polymorphism. Standard errors on such estimates are large, but the data have shown some consistencies. The mitochondrial genome is always more variable than nuclear DNA. Some estimates of nuclear genetic diversity are, of course, biased in that the estimates of Neμ are based on allozyme polymorphism and consequently do not include information about introns and noncoding sequences. Indeed, even in cases where Neμ has been estimated from restriction endonuclease map data the region in question has not been chosen at random from the whole genome and invariably contains coding sequences even though these may constitute only a proportion of the total map of particular interest. Nonetheless, the fact that 2Neμ/Nfμ is consistently very much less than 4 for such phylogenetically distinct species can be reasonably explained on the basis of higher mutation rates and mtDNA replication repair processes in the mitochondrial genome, rather than any variations in reproductive biology or sex-ratio imbalance which would be expected to lead more to variation in 2Neμ/Nfμ among species. Hence the mitochondrial genome can be expected to evolve at a much faster rate than the nuclear genome, both in terms of the rate of gene substitution and an increase in the rate of loss of neutral alleles.
Chloroplast DNA and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
During the last 25 years plant systematists have increasingly supplemented traditional biosystematic approaches with biochemical studies aimed at elucidating the phylogenetic significance of variation in the pattern and distribution of plant chemical constituents. The greatest number of these studies have involved the vast array of plant micromolecules (secondary plant products).1–3 Other studies have analyzed protein variation through serological comparisons,4 allozyme electrophoresis2,5,6 and amino acid sequencing,7 and DNA variation through DNA-DNA and DNA-RNA hybridization.2,8
Pseudoterranova
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Detection of allozyme markers by multilocus allozyme electrophoresis (MAE) permits differentiation among A. simplex, P. decipiens, and C. osculatum. Sequencing analysis of ribosomal RNA (18S, ITS1, 5.8S, ITS2, 28S), mitochondrial markers (cox1 and cox2), and other genes facilitates accurate taxonomic resolution and differentiation of sibling species [16,17].
Lowered PON1 activities are strongly associated with depression and bipolar disorder, recurrence of (hypo)mania and depression, increased disability and lowered quality of life
Published in The World Journal of Biological Psychiatry, 2019
Estefania Gastaldello Moreira, Dalmo Guilherme Correia, Kamila Landucci Bonifácio, Juliana Brum de Moraes, Fernanda Liboni Cavicchioli, Carolina Sampaio Nunes, Sandra Odebrecht Vargas Nunes, Heber Odebrecht Vargas, Décio Sabbatini Barbosa, Michael Maes
Blood was sampled after overnight fast. PON1 status was determined through three kinetic assays (Richter et al. 2008). To stratify individuals in the functional genotypes for the PON1 Q192R polymorphism (QQ, QR and RR) the substrates used were phenylacetate (PA, Sigma, USA) and 4-(chloromethyl)phenyl acetate (CMPA, Sigma, USA). CMPA is an alternative to the use of the toxic paraoxon. Q allozyme presents low efficacy to metabolise CMPA (or paraoxon), whereas both alloforms hydrolyse PA with approximately the same efficiency. The reaction with PA is conducted under high salt condition in order to partially inhibit the activity of the R allozyme, thus providing a better resolution of the three functional genotypes. The analysis was conducted in a spectrophotometer microplate reader (EnSpire, Perkin Elmer, USA). All assays were carried out in triplicate and a replicate that varied by 10% or greater was repeated. The results obtained with these two assays were used to plot a two-dimensional enzyme activity graphic that displays rates of PA hydrolysis under high salt conditions versus CMPA hydrolysis. Supplemental Figure 1A (available online) shows the classification of the subjects from this study. A third assay that measures rates of PA hydrolysis at low salt concentration reveals plasma PON1 total activity since under this assay condition, the PON1 Q192R polymorphism does not influence PON1 catalytic activity against PA (Furlong et al. 2006). Supplemental Figure 1B shows the total PON1 activity across the different PON1 Q192R genotypes.
Changes in lipid profile parameters and PON1 status associated with L55M PON1 polymorphism, overweight and exposure to tobacco smoke
Published in Inhalation Toxicology, 2018
Anna Bizoń, Monika Ołdakowska, Halina Milnerowicz
About 200 single nucleotide polymorphisms (SNPs) in promoter and coding regions have been identified in the human PON1 gene (Eom et al., 2011). The PON1 coding region has two major kinds of polymorphisms: L55M (163 T > A) and Q192R (575 A > G) (Mackness et al., 1998). In L55M, codon 55 leucine (L) is replaced by methionine (M) (Chen et al., 2018). L55M polymorphism (rs854560) does not affect the interaction of the enzyme with its substrates, but it does affect PON1’s mRNA levels and contribute to lower PON1 concentration and activity. It has been shown that the MM homozygote is related to lower levels of the enzyme’s activity and concentration and to lower levels of its mRNA (Rajkovic et al., 2011). The LL55 homozygote is more stable and resistant to proteolysis, which may partly explain the association of this alloenzyme with higher concentrations of PON1 in the serum (Rajkovic et al., 2011).
Association of PON1, TNF-α and TGF-β gene polymorphisms with prognosis in oral and oropharyngeal squamous cell carcinoma
Published in Acta Odontologica Scandinavica, 2021
Ingrede Tatiane Serafim Santana, José Nilson Andrade dos Santos, Vinicius Lima de Almeida, Waldhenice Nunes Silveira Ferreira, Edilmar Moura Santos, Roseana de Almeida Freitas, Claudia Cristina Kaiser Pinto, Ikaro Daniel de Carvalho Barreto, Felipe Rodrigues de Matos
A systematic review with meta-analysis did not reveal a protective or risk character for the SNP rs662 [28]. A possible explanation for the discrepancy of data found in the literature is that alloenzyme encoded by the T allele hydrolyses different substrates, such as paraoxon, more rapidly than the enzyme associated with the C allele. However, isoenzyme C is more efficient in protection against low-density lipoproteins oxidation [29].