Uri Gophna

Planetary-scale metagenomic search reveals new patterns of CRISPR targeting

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

Temporal dynamics of RNA phage infection reveal bacterial recovery despite ongoing viral replication

The paper studies RNA phage infection dynamics in E. coli, showing bacterial population rebound despite viral replication and cell death.

Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials

CRISPR-Cas targeting in Haloferax volcanii promotes within-species gene exchange by triggering homologous recombination

This study shows CRISPR-Cas targeting in Haloferax volcanii increases within-species mating and recombination, promoting gene exchange while limiting inter-species transfer.

A TIR-SAVED effector mediates antiviral immunity via a conserved host signal

This study shows a TIR-SAVED effector can act independently as an antiviral defense, clearing viruses without its cyclase partner and using a host-produced second messenger.

Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system

The paper identifies Cas11b as an internally translated protein in an archaeal CRISPR-Cas system, showing its necessity for effective interference and Cascade complex formation.

Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea

The paper identifies a provirus-encoded CRISPR-Cas system in Haloferax lucentense and shows it relies on a plasmid-encoded system for adaptation, suggesting horizontal transfer and cooperative immunity.

Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle

The paper identifies point-mutant cheater viruses in MS2 bacteriophage that disrupt the replication cycle with dual defects and advantages, and shows helper mutations often co-occur nearby.

Optimized Plaque Assay for Detecting Chronically Infecting Viruses of Haloarchaea

This paper develops an optimized plaque assay to detect chronically infecting haloarchaeal viruses by modifying agar concentration and incubation temperature, successfully identifying two viruses and enabling novel virus discovery.

An archaeal CBASS shows protective activity against both chronic and lytic viruses

This study shows that the archaeal CBASS system H-CBASS2 protects against both lytic and chronic viruses by depleting NAD+, with different kinetics depending on infection type.

Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei

This study compares homologous recombination and heteropolyploidy maintenance between Haloferax volcanii and Haloferax mediterranei, finding differences in recombination rates and genetic linkage.

Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations

The paper analyzes E. coli genomes from IBD patients to identify disease-specific genomic adaptations and their functional implications.

Direct Sequencing of RNA with MinION Nanopore: Detecting Mutations based on Associations

The paper introduces AssociVar, a statistical method to detect true mutations from MinION sequencing data by distinguishing them from random sequencing errors.

Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat

The study shows that colony-level dynamics, not individual-level changes, drive fur microbiome variation in Egyptian fruit bats, suggesting the colony as a biological unit for studying host-microbiome interactions.

Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids.

This study measures allele-specific expression in archaeal hybrids to reveal cis-regulatory evolution in prokaryotes, finding lineage-specific selection on kinase genes under low phosphate conditions.