J. Vogel

The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization

This study identifies a small RNA, SrcF, essential for gut colonization of Segatella copri, regulated by complex carbohydrates and influenced by the human microbiome.

A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

The paper identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum through mass spectrometry analysis of sRNA interactors.

Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa

This study uses ONT-cappable-seq to map transcriptional landscapes of six Pseudomonas aeruginosa phages, revealing new regulatory elements and gene expression mechanisms.

Global RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery

This study maps the Hfq-mediated RNA interactome in nitrogen-starved E. coli, revealing SdsR's role in post-transcriptional regulation during long-term growth arrest and recovery.

A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics

This study compares seven chemically distinct antisense oligomers targeting Salmonella acpP, finding only PNA and PMO are effectively delivered by a KFF peptide to inhibit bacterial growth.

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have sub-minute half-lives

The paper develops a Bayesian model to estimate RNA stability in Salmonella, revealing most transcripts have sub-minute half-lives and RBPs significantly affect decay rates.

Immediate targeting of host ribosomes by jumbo phage encoded proteins

This study identifies phage-encoded proteins that target host ribosomes to modulate translation in Pseudomonas aeruginosa.

Microbial fingerprints reveal interaction between museum objects, curators and visitors

The paper uses microbial signatures from museum objects to identify human contact patterns and differentiate between individuals' touch.

Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads

This paper improves bacterial single-cell RNA-seq by automating MATQ-seq and using Cas9 to remove rRNA, enhancing gene detection and reducing cell loss.

Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens

This study uses Grad-seq to identify RNA-protein complexes and novel sRNAs in E. faecalis and E. faecium, revealing conserved regulatory mechanisms and potential roles of KhpB in RNA processing.

PHYTOCHROME C regulation of PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon

This study shows that PHYTOCHROME C activates PHOTOPERIOD1 via EARLY FLOWERING 3 in Brachypodium distachyon, revealing ELF3 as a repressor of PPD1 in the photoperiod flowering pathway.

New genetic tools enable dissection of a global stress response in the early-branching species Fusobacterium nucleatum

The paper develops genetic tools for Fusobacterium nucleatum and identifies a sigmaE-mediated stress response involving a conserved non-coding RNA.

INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

The paper introduces INRI-seq, a cell-free Ribo-seq method to study translation initiation and off-target effects of antisense inhibitors in E. coli.

Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli

This study systematically evaluates PNA-based antisense antibiotics targeting essential genes in UPEC, identifying effective targets and revealing bacterial responses to PNA conjugates.

Contact sites between endoplasmic reticulum sheets and mitochondria regulate mitochondrial DNA replication and segregation

The paper shows that ER sheet-mitochondria contact sites regulate mtDNA replication and distribution, with DRP1 loss disrupting this interaction and causing mtDNA issues.

Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease

This study identifies ProQ residues critical for function and reveals that Lon protease mediates quality control of ProQ and Hfq by degrading non-functional RNA-binding proteins.

Tracking the Ancestry of Known and 'Ghost' Homeologous Subgenomes in Model Grass Brachypodium Polyploids

The paper identifies subgenomes in Brachypodium polyploids using phylogenomic methods and confirms the existence of ancestral genomes in polyploids.

RNase E endonuclease activity and its inhibition by pseudoridine

This study investigates RNase E's endonuclease activity, its inhibition by pseudouridine, and its interaction with partner proteins in the RNA degradosome.

REDUCED ER-MITOCHONDRIA CONNECTIVITY PROMOTES NEUROBLASTOMA MULTIDRUG RESISTANCE

The paper identifies reduced ER-mitochondria contacts as a mechanism promoting neuroblastoma multidrug resistance by impairing Ca2+ transfer and apoptosis.

MAPS integrates overlooked regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT

The paper identifies PinT as a regulator of SteC in Salmonella, revealing its role in suppressing actin rearrangements during infection.

Spindle alignment is uncoupled with Kar9 symmetry breaking

The paper quantifies Kar9 symmetry breaking in budding yeast and finds it is not tightly coupled with early spindle alignment, suggesting Kar9 asymmetry alone is insufficient for stable spindle alignment.

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important Gram-positive bacterium

This study maps the transcriptome of C. difficile and reveals Hfq's role in post-transcriptional regulation through RNA-centric techniques and Hfq RIP-seq.

A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells

This study maps direct RNA-protein interactions of SARS-CoV-2 RNA in infected human cells using RAP-MS, identifying host factors, regulators, and potential drug targets involved in viral replication and host defense.

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

The paper uses Grad-seq to map RNA/protein complexes in E. coli, identifying new interactions and reclassifying RNA functions.

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

The paper introduces GradR, a method combining RNase treatment and mass spectrometry to discover bacterial RNA-binding proteins, identifying FopA as a new FinO domain RBP with distinct RNA targets.

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

The paper identifies and characterizes small proteins in Salmonella Typhimurium using integrated omics data, revealing a new role for MgrB in virulence and motility.

Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi

The paper uses dual RNA-seq to study the transcriptional architecture and host-pathogen interactions of Orientia tsutsugamushi, identifying antisense regulation and strain-specific immune responses.

Kinesin-5 forms a stable bipolar spindle in a fast, irreversible snap

The paper shows Kinesin-5 crosslinking drives fast, irreversible pole separation in monopolar spindles, forming a stable bipolar spindle.

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

The paper shows that Brachypodium distachyon consistently responds to soil conditions across labs, depleting soil metabolites and altering root morphology.

Cross-species functional diversity within the PIN auxin efflux protein family

The paper investigates functional differences between SoPIN1 and PIN1b in grasses and Arabidopsis, showing distinct roles in organ initiation and stem growth.