Biology subjects

Baehr, S.

Publications and source records attributed to Baehr, S..

4 recordsLinked to original sources

bioRxiv2026

Evolution of the highest fidelity DNA replication systems

DNA mutation on average is deleterious, and evolution generally acts to reduce mutation rates to the limit of natural selection. The limit of natural selection is set by multiple factors, of which effective population size is only one. We consider lethal mutagenesis as an upper bound to mutation rates for any organism, an argument that is congruent with a biophysical context, wherein random mutations are a form of entropy. In this analysis, coding genome size, body mass, generation time, and temperature potentially explain more than 90% of the variation in mutation rate per generation across the Tree of Life. The organisms with larger genomes, longer lifespans and relatively larger body sizes, known and unknown, represent the lineages which have likely evolved novel mechanisms to lower mutation rates, a desirable trait for reducing cancer incidence. Though these variables are largely shared by Petos Paradox, this selective pressure responsible for the evolution of lower mutation rates occurs through germline mutation rate evolution rather than the soma. SignificanceDNA replication varies and is influenced by natural selection. Mutations are usually harmful and contribute to human diseases like cancer, Understanding the evolutionary factors behind DNA replication fidelity may help identify and develop novel strategies to reduce human mutation rates.

molecular biology↗

bioRxiv2025

DNA Circle-sequencing lowers the single molecule sequencing error threshold and identifies ultrasonication as a source of DNA damage

DNA mutation is the ultimate source of all heritable genetic and phenotypic variation. On human timescales, DNA mutation results in the evolution of antibiotic resistance, viral resistance to vaccines, the emergence human cancers, and more. Precise measurement of DNA mutation is therefore desirable to rapidly detect and analyze low frequency mutations in a population of cells. Precise measurement of DNA mutation by high throughput sequencing has been hindered by sequencing error rates, which occur at rates 1x10-2 to 1x10-3 per base sequenced. Previous work on circle sequencing had pushed a putative sequencing error rate down to roughly 2.8x10-4 per base for genomic yeast DNA in the absence of DNA repair enzymes, where the expected number is 4.7x10-9 per base per generation. Through revision of the assay, we are now capable of taking 125ng of genomic DNA and obtaining mutation rate estimates with a sequencing resolution floor of 2x10-7 per base in the absence of repair enzymes, a resolution improvement of over 3 orders of magnitude. In practice, circle-seq recovers some of the mutation spectrum of mismatch-repair deficient E. coli, although some signature of C [->] T and G [->] A errors remain present. Curiously, it calls a mutation rate of 2x10-9 per base per generation, lower than expected, underscoring the difficulty of directly comparing mutation rates per base to MA mutation rates per site per generation. This protocol readily recognizes Covaris ultrasonication as mutagenic in library preps, with a mutation spectrum dominated by G:C [->] A:T, G:C [->] C:G, and G:C [->] T:A errors. The protocol is either detecting in vivo DNA damage that has yet to be repaired, is significantly biased in its ability to detect mutations, or is not yet sensitive enough to detect mutation rates of MMR-E. coli cells. The protocol may have some use in measuring mutation abundance from tissue samples, and in vitro sources of DNA damage. The protocol also highlights some biases inherent to single-stranded DNA (ssDNA) cyclization, including a 10-bp periodicity which echoes the constraints of dsDNA cyclization.

molecular biology↗

bioRxiv2023

Consideration of a liquid mutation accumulation experiment to measure mutation rates by successive serial dilution.

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though it is laborious to perform. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of real environmental living conditions. We propose that a fully liquid-phase mutation-accumulation experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR- E. coli in liquid LB culture vs. plate LB culture. We detect a modified mutation spectrum with a transition skew of 4:1 of A:T[->]G:C vs G:C[->]A:T mutations, highlighting the potential role of tautomerization as a DNA mutation mechanism. We also find that using a plate reader to measure OD600 as a proxy for cell growth to be incapable of measuring carrying capacity for MA lines burdened with many mutations.

microbiology↗

bioRxiv2023

A Narrow Range of Transcript-error Rates Across the Tree of Life

The expression of genomically-encoded information is not error-free. Transcript-error rates are dramatically higher than DNA-level mutation rates, and despite their transient nature, the steady-state load of such errors must impose some burden on cellular performance. However, a broad perspective on the degree to which transcript-error rates are constrained by natural selection and diverge among lineages remains to be developed. Here, we present a genome-wide analysis of transcript-error rates across the Tree of Life using a modified rolling-circle sequencing method, revealing that the range in error rates is remarkably narrow across diverse species. Transcript errors tend to be randomly distributed, with little evidence supporting local control of error rates associated with gene-expression levels. A majority of transcript errors result in missense errors if translated, and as with a fraction of nonsense transcript errors, these are underrepresented relative to random expectations, suggesting the existence of mechanisms for purging some such errors. To quantitatively understand how natural selection and random genetic drift might shape transcript-error rates across species, we present a model based on cell biology and population genetics, incorporating information on cell volume, proteome size, average degree of exposure of individual errors, and effective population size. However, while this model provides a framework for understanding the evolution of this highly conserved trait, as currently structured it explains only 20% of the variation in the data, suggesting a need for further theoretical work in this area.

evolutionary biology↗