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Diagnosis and Pathobiology
Published in Franklyn De Silva, Jane Alcorn, The Elusive Road Towards Effective Cancer Prevention and Treatment, 2023
Franklyn De Silva, Jane Alcorn
The epigenetic machinery can be separated into a number of interconnected components such as histone PTMs, DNA methylation (the most well-studied epigenetic alteration), noncoding RNAs (ncRNAs), and undercharacterized modifications (not discussed here) such as chromatin modifications, chromatin accessibility, histone (H) variants (e.g., H3.3, H2A.X, H2A.Z), and RNA modifications (e.g., N6-methyladenosine (m6A)) [296, 364, 367, 391, 393, 399, 402]. Many epigenetic modifications involve covalent bond modifications; however, the main noncovalent epigenetic mechanisms include incorporation of histone variants, nucleosome remodeling, and noncoding RNAs [369]. Chromatin structure and gene expression are regulated by specific amino acids of histone protein tails (consisting of 15–38 amino acids) that undergo various PTMs [366]. Due to the complex diversity among PTMs, the following are considered types of acylation: acetylation, propionylation, butyrylation, crotonylation, 2-hydroxy isobutyrylation, malonylation, succinylation, and glutarylation [403]. Ubiquitylation, sumoylation of lysine residues, and phosphorylation of serine (S) and threonine (T) residues, as well as formylation, O-GlcNAcylation, propionylation, adenosine diphosphate (ADP)-ribosylation, deamination, proline/aspartic acid isomerization, citrullination/eamination, biotinylation, and crotonylation, are reported histone modifications (>200 known modifications) that occur at more than 60 amino acid residues [296, 364, 386, 387, 394, 395].
Cytochrome c
Published in Robert A. Greenwald, CRC Handbook of Methods for Oxygen Radical Research, 2018
Reduced cytochrome c can be reoxidized by cytochrome oxidases and peroxidase. To the extent that this occurs in a reaction mixture, the rate of accumulation of ferrocytochrome c will be diminished and the rate of production of O2− will be underestimated. There are several strategies which have proven useful in minimizing this source of error. One of these uses CN− or N3− at levels which largely inhibit cytochrome c oxidases and peroxidases, but which only minimally interfere with other components of the test system. Another uses cytochrome c which has been modifed by acylation of ϵ-amino groups of lysine residues. Both acetylation4 and succinylation5 have been used and the acylated cytochrome c is advantageous in that it remains reducible by O2−, albeit at a slower rate, while no longer serving as a substrate for cytochrome c oxidase or for NADH cytochrome c reductase.
Cyclic Nucleotide Metabolism and Action During Senescence
Published in Richard C. Adelman, George S. Roth, Endocrine and Neuroendocrine Mechanisms of Aging, 2017
Assays of absolute levels of cyclic nucleotides are based upon the concentration-dependent inhibition by cyclic nucleotide containing extracts of binding of either 3H-cyclic nucleotide to a partially purified binding protein or of an l25I-cyclic nucleotide analogue to an antibody.8 The binding protein method was developed first and, though somewhat less sensitive than the radioimmunoassay, continues to be used where high sensitivity is not required and cost is a factor. Greater sensitivity and specificity is obtained with the radioimmunoassay technique as a consequence of acetylation or succinylation of extracted cyclic nucleotides. While this may permit considerable dilution of samples and results in fewer problems of interference by reagents or unknown contaminants, the possibility of interfering substances in extracts must still be checked.9 This is done by determining that measured levels of cyclic nucleotide are proportional to the amount of extract used, i.e., that the slope or shape of the inhibition curve is the same as that of a standard curve based on a pure solution of cyclic nucleotide. Where it occurs, interference may depend upon the concentration of the extract, the type of tissue extracted, or the extraction reagents. The problem is usually resolved by purification of extracts through one or a combination of chromatographic steps.10,11 Purification may be accomplished with11 or without neutralization of acid extracts,10 depending on the method chosen. When the radioimmunoassay method is used, the dilution of extract occurring at this step may present no problem and alleviate the need for lyophilization and redissolution in small volumes. Analysis of the actual data may be facilitated and performed more accurately by linearization of the data, perhaps best done with a curve-fitting program described by Brooker et al.8
Pullulan based derivatives: synthesis, enhanced physicochemical properties, and applications
Published in Drug Delivery, 2022
Surendra Agrawal, Divya Budhwani, Pravina Gurjar, Darshan Telange, Vijay Lambole
Periodate oxidation involves introducing the aldehyde group in pullulan, making pullulan capable of carrying macromolecules (Bruneel & Schacht, 1993). A scaffold was prepared using pullulan with collagen and loaded with lysine or hydroxylysine by freeze-drying method. The scaffold resulted in enhanced crosslinking due to the reaction of aldehyde of oxidated pullulan and amino group of lysine or hydroxylysine. The enhanced crosslinking decreases the rate of degradation. This indicated pullulan as promising bio-crosslinked for biomaterial synthesis (Selvakumar & Lonchin, 2020). Succinylation involves the introduction of a hydrophobic substance to pullulan, which can encapsulate hydrophobic and charged protein.