N. Neff

How Mycobacterium tuberculosis builds a home: Single-cell analysis reveals M. tuberculosis ESX-1-mediated accumulation of anti-inflammatory macrophages in infected mouse lungs.

This study uses single-cell RNA sequencing to show that M. tuberculosis ESX-1 promotes the recruitment and differentiation of anti-inflammatory macrophages in infected mouse lungs.

PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2

RMC-113 inhibits PIP4K2C and PIKfyve, reversing SARS-CoV-2-induced autophagic flux impairment and showing antiviral effects.

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

This study investigates gut microbiome colonization dynamics after antibiotic use, finding prolonged delays in microbial transmission and ecological barriers to colonization.

Cholangiocytic differentiation drives cell proliferation in hepatoblastoma through Wnt-dependent FGF19 signaling

The paper identifies FGF19 as a paracrine signal driving tumor growth in hepatoblastoma through Wnt-dependent mechanisms and biliary lineage activation.

Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics

This study shows that gut microbiota assembly follows 'early-bird' dynamics where fast-growing species dominate nutrient sources, and develops a predictive model for community composition based on nutrient inputs.

Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution

This study analyzes single-cell transcriptomes of primary tumors and metastases from breast cancer models, identifying transcriptional differences and gene signatures linked to metastatic potential and patient outcomes.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

This study compares infant gut microbiome assembly in Hadza hunter-gatherers and industrialized infants, finding distinct microbial trajectories and functional differences.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

The paper uses ultra-deep metagenomic sequencing to analyze the gut microbiome of Hadza hunter-gatherers, revealing many microbes absent from existing datasets and highlighting differences in microbial dynamics compared to industrialized populations.

Hepatitis C Virus Infects and Perturbs Liver Stem Cells

This study identifies liver stem cells as targets of HCV infection, showing their transcriptional reprogramming and role in liver damage and cancer risk.

Intermittent fasting induces rapid hepatocyte proliferation to restore the hepatostat in the mouse liver.

This study shows intermittent fasting induces rapid hepatocyte proliferation in mice to maintain liver-to-body-mass ratio, challenging the view that liver tissue is quiescent unless injured.

In vivo augmentation of a complex gut bacterial community

The paper improves a synthetic gut microbiota community by adding strains that persist after fecal challenge and removing those that do not, resulting in a more stable model of the human gut microbiome.

Systematic dissection of a complex gut bacterial community

This study constructs a defined gut bacterial community of 104 strains and investigates strain-strain and strain-nutrient interactions through amino acid dropout experiments.

Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

The paper tracks bacterial evolution and transmission in mice using barcoded E. coli strains, showing rapid selection and migration effects on microbiota composition.

Bacterial evolution in high osmolarity environments

This study evolves Escherichia coli in high osmolarity environments and finds that adaptation strategies vary by osmolyte, with specific mutations improving fitness in certain conditions.

High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

This study develops a high-throughput method to cultivate diverse, stable fecal-derived microbial communities in vitro, demonstrating their utility for modeling the intestinal microbiota and predicting in vivo responses to antibiotics.

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

This study investigates how ageing affects mouse thymus function, revealing that progenitor cell differentiation is disrupted, leading to impaired T cell selection and self-antigen representation.

Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing

This study uses longitudinal single-cell RNA sequencing to reveal therapy-induced adaptations in lung cancer, identifying cell state transitions and pathways associated with treatment response and resistance.

Humans are colonized by many uncharacterized and highly divergent microbes

The paper identifies hundreds of new bacteria and viruses in the human microbiome using blood-based shotgun sequencing and validates their existence through independent experiments and PCR.