Biology subjects

Davis, M. W.

Publications and source records attributed to Davis, M. W..

5 recordsLinked to original sources

bioRxiv2025

Delineating Mutation Bias and Selection during Plant Development

Plants accumulate germline mutations through meristematic lineages where somatic purifying selection could remove deleterious coding mutations and produce perceived mutation biases, like lower genic mutation rates. Here we describe a quantitative framework that uses mutation spectra and genome architecture to separate missing coding mutations from true genic hypomutation for selection-corrected estimates of mutation biases. In simulations of plant meristems subject to selection and mutation bias, only extremely strong dominant mutations produced gene-body patterns in the same direction as empirical estimates of hypomutation. However, after accounting for this selection, we can recover the true underlying mutation rate variation. We apply this to re-analysis of Arabidopsis mutation-accumulation datasets. After selection, we see [~]50% lower mutation rates in gene bodies and an additional [~]15-30% reduction in broadly expressed genes, consistent with mutation rate bias. This framework provides a quantitative method to compare mutation rates across the genome while explicitly controlling for selection on coding sequence mutations.

plant biology↗

bioRxiv2025

Extreme somatic mutation variation through time and space in walnut clones

Many plants, unlike most animals, can reproduce as clones1. Cloning plants is critical for agriculture2,3 and biotechnology4, but the extent of somatic mutation arising during different propagation methods remains an important question for both fundamental research and agriculture. Here, we discover a surprisingly complex mutational history in a multi-decade natural experiment of isogenic walnut clones derived and maintained through three alternative methods: budwood propagation of field-grown trees, in vitro shoot culturing, and in vitro somatic embryogenesis. We generated a haplotype-phased reference genome assembly and revealed a >3500% increase in somatic embryo mutation rates compared to field-grown trees, along with a distinct mutation spectrum. The assembly also helped reveal extreme genomic instability in the somatic embryos, including multiple chromosomal duplications, megabase-scale deletions, telomere expansions, somatic recombination events, and ongoing transposable element activation. Our survey of somatic mutation also provides high-resolution insight into clonal stem cell dynamics, confirming the canonical meristem layers of flowering plants in the tree and shoot clones, while uncovering clear evidence of frequent single-cell bottlenecks in the somatic embryos. These discoveries inform practical questions about mutagenesis through plant tissue culture and serve as a benchmark to complement emerging paradigms of somatic mutation research in humans and other organisms.

genomics↗

bioRxiv2021

High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome

Gene editing in C. elegans using plasmid-based CRISPR reagents requires microinjection of many animals to produce a single edit. Germline silencing of plasmid-borne Cas9 is a major cause of inefficient editing. Here, we present a set of C. elegans strains that constitutively express Cas9 in the germline from an integrated transgene. These strains markedly improve the success rate for plasmid-based CRISPR edits. For simple GFP insertions, 60 - 100% of injected animals typically produce edited progeny, depending on the target locus. Template-guided editing from an extrachromosomal array is maintained over multiple generations. We have built strains with the Cas9 transgene on multiple chromosomes. Additionally, each Cas9 locus also contains a heatshock-driven Cre recombinase for selectable marker removal and a bright fluorescence marker for easy outcrossing. These integrated Cas9 strains greatly reduce the workload for producing individual genome edits. Author SummaryGermlines have evolved specialized mechanisms to protect themselves from invasions by transposons and viruses, which create barriers to genome editing techniques. For example, transgenes are silenced in the germline of the nematode C. elegans, thereby creating a barrier to CRISPR editing by Cas9. To facilitate gene editing, we built a collection of C. elegans strains in which Cas9 is never silenced. CRISPR is significantly more efficient in these animals, decreasing the effort researchers need to expend to get edited animals. The strains are available in multiple genetic backgrounds, and contain accessory transgenes to simplify downstream genetics. Together, these strains enable efficient, low-cost genome editing in C. elegans.

genetics↗

bioRxiv2020

SynapsEM: computer-assisted synapse morphometry

The structural features of a synapse, in part, determine its output. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified using morphometry. Three parameters are typically assessed from each specimen: 1) the sizes of individual vesicles and organelles, 2) the absolute number and densities of organelles, and 3) distances between organelles and key features at synapses such as active zone membranes and dense projections. For data to be valid, the analysis must be repeated from hundreds or thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze these features: SynapsEM. In short, we developed macros for ImageJ/Fiji to record x,y-coordinates of segmented structures; the coordinates are then exported as text files. Independent investigators can reload the images and text files to confirm or re-evaluate the segmentation using ImageJ. The Matlab program calculates and reports key synaptic parameters from the coordinates. Since the values are calculated, rather than measured from each micrograph, other parameters can be extracted in Matlab by additional scripting. Thus, this program can accelerate morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.

neuroscience↗

bioRxiv2018

Synaptic vesicles undock and then transiently dock after an action potential

Synaptic vesicles fuse with the plasma membrane to release neurotransmitter following an action potential, after which new vesicles must dock to refill vacated release sites. To capture synaptic vesicle exocytosis at cultured mouse hippocampal synapses, we induced single action potentials by electrical field stimulation then subjected neurons to high-pressure freezing to examine their morphology by electron microscopy. During synchronous release, multiple vesicles can fuse at a single active zone; this multivesicular release is augmented by increasing extracellular calcium. Fusions during synchronous release are distributed throughout the active zone, whereas fusions during asynchronous release are biased toward the center of the active zone. Immediately after stimulation, the total number of docked vesicles across all synapses decreases by [~]40%. Between 8 and 14 ms, new vesicles are recruited to the plasma membrane and fully replenish the docked pool in a calcium-dependent manner, but docking of these vesicles is transient and they either undock or fuse within 100 ms. These results demonstrate that recruitment of synaptic vesicles to release sites is rapid and reversible.

neuroscience↗