D. Gresham

Template switching during DNA replication is a prevalent source of adaptive gene amplification

The paper investigates how genomic architecture influences the formation and fitness of adaptive copy number variants (CNVs) in yeast, finding that template switching during DNA replication is a common mechanism for CNV generation.

Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence

This study uses proteomics and phosphoproteomics to show that carbon and phosphorus starvation trigger distinct but overlapping molecular processes in yeast quiescence.

Host obesity impacts genetic variation in influenza A viral populations

This study investigates how host obesity affects genetic variation in influenza A virus populations using a ferret model, finding enhanced positive selection and host-specific mutations in obese hosts.

mRNA condensation fluidizes the cytoplasm

The paper shows that stress-induced mRNA condensation increases mesoscale diffusivity in the cytoplasm, fluidizing it and aiding in the formation of Q-bodies.

Increased mesoscale diffusivity in response to acute glucose starvation

The paper examines how acute glucose starvation affects the diffusivity of macromolecules and fluorescent nanoparticles, finding reduced mRNP diffusivity and increased NS particle diffusivity.

Influenza A virus reassortment is strain dependent

This study quantifies reassortment rates among diverse influenza A strains and finds strain-specific biases in reassortment, independent of subtype or coinfection partner.

Simulation-based inference of evolutionary parameters from adaptation dynamics using neural networks

The paper estimates beneficial mutation rates and fitness effects using simulation-based Bayesian inference on CNV dynamics in yeast.

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data

This study evaluates variant calling tools for detecting minority variants in viral sequencing data and provides guidance for accurate quantification of intrahost viral diversity.

Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection

The paper shows fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection, contrasting with static environments that reduce diversity.

Microbial community structure and ecology in sediments of a pristine mangrove forest

This study examines microbial community structure and ecology in mangrove sediments, finding that submerged regions have the highest diversity and richness, while intertidal regions show the lowest diversity.

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

This study detects single-cell copy number variants (CNVs) in evolving populations and identifies ODIRA as a common mechanism for gene amplification.