Journal: Chemical research in toxicology

Article Title: Establishing Linkages Among DNA Damage, Mutagenesis, and Genetic Diseases

doi: 10.1021/acs.chemrestox.2c00155

Figure Lengend Snippet: Technologies discussed in this paper. (A) Mutational spectra classically are produced by damaging the genome of a cell or vector and replicating the damaged piece of DNA in cells that have normal or disabled DNA repair status or normal or altered replicative status. Mutations are determined and plotted along the sequence of the piece of DNA as shown. (B) Often it is of value to test the hypothesis that a given mutation might have been caused by a specific DNA adduct. In that case, an oligodeoxynucleotide is synthesized with the adduct at a specific site. The oligonucleotide is spliced into the genome of a vector, usually a plasmid or viral genome, and replicated in living cells. Mutant progeny are sequenced. The type, amount and genetic requirements for mutagenesis are thereby determined, along with the potential genotoxicity of the lesion. Most of the lesions discussed in the text were evaluated by this site-specific mutagenesis strategy.

Article Snippet: Yet, at the time we wrote the original paper, we could not anticipate the discovery of an entire family of lesion bypass polymerases (the Y-family DNA polymerases), the impressive progress in mass spectrometry and high-throughput DNA sequencing (NextGen sequencing) as well as other advances that occurred to bring the field to its present state.

Techniques: Produced, Plasmid Preparation, Sequencing, Mutagenesis, Synthesized

Journal: Mammalian Genome

Article Title: Genome characterization of the selected long- and short-sleep mouse lines

doi: 10.1007/s00335-016-9663-6

Figure Lengend Snippet: Differences between ILS and ISS strains: Variant Breakdown. a Combined totals of variants that differ between the ILS and ISS strains. Synonymous mutations refer to a SNP(s) that alters the codon sequence but not the amino acid produced. Synonymous and non-synonymous mutations arise from the impact of a SNP on the underlying codon. Frameshifts are any indel not divisible by three, whereas deletions and insertions retain the reading frame. Variants are counted once per gene. b Combined totals of structural variations that differ between ILS and ISS strains. Losses and gains refer to changes in copy number, whereas a deletion is a complete loss/absence of a region. Chromosomal translocations refer to exchanges of large segments between chromosomes and inversions are reversals. c Distribution of structural variations by type, summarized by a sliding window approach (500 k windows with 100 k step size) (Color figure online)

Article Snippet: However, technological and analytical advances, including high-throughput gene expression analysis and “Next-Generation” deep sequencing technologies (NextGen), are providing an unprecedented opportunity to examine the molecular basis of QTLs (Harrison ).

Techniques: Variant Assay, Sequencing, Produced