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Basic Microbiology
Published in Philip A. Geis, Cosmetic Microbiology, 2020
Nucleoid—Although bacteria do not have a membrane-bound nucleus where DNA is contained, the bacteria do organize and compartmentalize their DNA. The nucleoid is a DNA-rich region within the bacteria cell where DNA has been compacted to allow it fit within the cell. Rather than being haphazardly condensed, bacterial nucleoids have specific sequences contained within specific areas of the nucleoid to optimize the use of DNA.
Topoisomerase II Inhibition by Antitumor Intercalators and Demethylepipodophyllotoxins
Published in Robert I. Glazer, Developments in Cancer Chemotherapy, 2019
Nucleoids are cell nuclei from which essentially all of the proteins except those of the scaffold have been removed. Nucleoids are prepared by disruption of the cell membrane with a nonionic detergent (Triton® X-100) and exposure to 2 M NaCl, which dissociates nearly all of the chromosomal proteins. The DNA remains intact, supercoiled, and attached to the structural scaffold, but is devoid of histones or nucleosomes.16,34,35
Mitochondrial Genome Damage, Dysfunction and Repair
Published in Shamim I. Ahmad, Handbook of Mitochondrial Dysfunction, 2019
Kalyan Mahapatra, Sayanti De, Sujit Roy
Mitochondrial DNA is compact and less than 20 kilo bases in length (Wolstenholme, 1992) encoding protein subunits of the mitochondrial respiratory chain (Okimoto et al., 1992). There also exist structures called nucleoids, which are mainly composed of 2-8mtDNAcopies (Legros et al., 2004). Nucleoids are associated with the inner mitochondrial membrane and distributed throughout the mitochondrial network at regular spatial intervals (Prachar, 2010). Generally, mitochondrial DNA is multi copied with a 16,569-bp double-stranded circular molecule located within the matrix of the mitochondrion, inherited from the maternal oocyte and is self-replicative.
Toxicological profile of lipid-based nanostructures: are they considered as completely safe nanocarriers?
Published in Critical Reviews in Toxicology, 2020
Asaad Azarnezhad, Hadi Samadian, Mehdi Jaymand, Mahsa Sobhani, Amirhossein Ahmadi
Cells embedded in agarose on a microscope slide are lysed with detergent and high salt to form nucleoids containing supercoiled loops of DNA linked to the nuclear matrix. In fact, electrophoresis of the genomic DNA of the target cells leads to the formation of a comet of the charged DNA particles moving on the electrophoresis gel, the comet that depends on the severity of the damage and the type of destructive agent. This is followed by visual analysis with the staining of DNA and calculating fluorescence to determine the extent of DNA damage. This can be performed by manual scoring or automatically by imaging software. Electrophoresis at high pH (alkaline condition) leads to structures resembling comets, observed by fluorescence microscopy. The intensity of the comet tail relative to the head reflects the number of DNA breaks (Collins 2004; Nandhakumar et al. 2011).
Bacterial death from treatment with fluoroquinolones and other lethal stressors
Published in Expert Review of Anti-infective Therapy, 2021
Studies of bacterial nucleoids demonstrate quinolone-mediated chromosome fragmentation. When cells are lysed gently in the absence of protein denaturants, nucleoids can be isolated in which the DNA is intact and negatively supercoiled. These structures are readily recovered when bacteriostatic concentrations of nalidixic/oxolinic acid are applied to cultures [19]. However, at high, lethal quinolone concentrations, nucleoid sedimentation rate decreases, supercoiling is lost, and chromosome fragmentation is detected [22,33]. Since unrepaired double-strand DNA breaks are lethal, chromosome fragmentation has been a reasonable explanation for quinolone-mediated killing. A key, unanswered question is how elevating the quinolone concentration causes chromosome fragmentation.
Track-structure simulations of energy deposition patterns to mitochondria and damage to their DNA
Published in International Journal of Radiation Biology, 2019
Werner Friedland, Elke Schmitt, Pavel Kundrát, Giorgio Baiocco, Andrea Ottolenghi
To help assess the initial mtDNA damage by ionizing radiation and its biological consequences, mechanistic modelling studies have been performed in this work. A novel model representing the structure of mitochondrial DNA has been developed and implemented in PARTRAC. Following experimental information, the model contains a closed 16.7 kbp DNA double helix in atomic resolution, which shows frequent turns imposed by bound TFAM proteins and forms a compact 60 nm nucleoid. Each mitochondrion contains several nucleoids (10 in the reported simulations). Energetically active cells such as cardiac muscle or liver cells include a high number of mitochondria per cell (1000 in this study).