J. Fu

RNA folding kinetics control riboswitch sensitivity in vivo

The paper shows that slowing RNA folding kinetics enhances riboswitch sensitivity in vivo and identifies general principles for programming RNA folding dynamics.

High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation

This study analyzes the gut microbiome of treated coeliac disease patients at strain level, revealing increased interindividual variation and specific microbial associations.

A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

The paper evaluates predictive models for immune checkpoint inhibitor outcomes in NSCLC using clinical trial data from two RCTs, finding that models combining PD-L1, TMB, and immune signatures outperform single biomarkers.

Neurotrophic factor Neuritin modulates T cell electrical and metabolic state for the balance of tolerance and immunity

This study shows that neuritin modulates T cell electrical and metabolic states, influencing immune tolerance and immunity.

Legionella pneumophila exploits the endo-lysosomal network for phagosome biogenesis by co-opting SUMOylated Rab7

This study identifies Hmg20a and Nol9 as host factors restricting L. pneumophila replication by repressing Rab7, which is co-opted by the bacterium via SulF to facilitate phagosome biogenesis.

A human pluripotent stem cell-based somitogenesis model using microfluidics

This study develops a microfluidic hPSC-based model to control biochemical and biomechanical signals during somitogenesis, revealing their roles in somite formation.

Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming

This study identifies SEMA3D as a dual driver of pancreatic ductal adenocarcinoma progression and metastasis through tumor- and nerve-derived mechanisms involving macrophage reprogramming.

Cytoskeletal activation of NHE1 regulates mechanosensitive cell volume adaptation and proliferation

This study identifies a mechanism where cytoskeletal activation of NHE1 drives secondary volume increase and affects cell proliferation in response to hypotonic stress.

Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life

Urban non-point source pollutants cause microbial community homogenization via increasing deterministic processes

This study shows urban non-point source pollutants homogenize microbial communities by increasing deterministic processes and reducing habitat heterogeneity.

Longer mandible or nose? Co-evolution of feeding organs in early elephantiforms

This study investigates the co-evolution of feeding organs in early elephantiforms, finding that feeding function shifted from the mandible to the trunk, enabling proboscideans to expand into new ecological niches.

Reprogramming Yarrowia lipolytica metabolism for efficient synthesis of itaconic acid from flask to semi-pilot scale

This study reprograms Yarrowia lipolytica metabolism to produce itaconic acid at high titres in bioreactors, offering a safer alternative to pathogenic fungal producers.

The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

The paper identifies cell-type specific gene expression and regulatory networks in bioenergy sorghum stems to enable engineering for biofuel production.

The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation

The paper shows that BOD1L in the SETD1A complex maintains DNA repair gene expression despite reducing H3K4 trimethylation, and its loss causes DNA damage and cell death in ESCs.

Dopamine receptor D2 confers colonization resistance via gut microbial metabolites

This study shows that dopamine receptor D2 mediates colonization resistance against gut pathogens via microbial metabolites.

The prospect of universal coronavirus immunity: a characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses

The paper investigates T cell cross-reactivity between SARS-CoV2 and common human coronaviruses, finding broad immunity in survivors and reduced omicron recognition in vaccinated individuals.

RecA balances genomic stability and evolution using many successive mismatch tolerant homology tests

The paper models how RecA in E. coli balances genomic stability and evolution by testing homology with increasing stringency, predicting that 50 bp of testing is needed for accurate allelic pairing.

Evaluation of antibody kinetics and durability in health subjects vaccinated with inactivated COVID-19 vaccine (CoronaVac): A cross-sectional and cohort study in Zhejiang, China

This study evaluates antibody kinetics and durability after CoronaVac vaccination in health subjects, finding waning antibody levels over time and improved responses with a booster dose.

The mechanism of nicotinamide phosphoribosyltransferase whereby positive allosteric modulation elevates cellular NAD+

This study identifies the mechanism by which NAMPT is activated by positive allosteric modulators, revealing how this enhances NAD+ biosynthesis and regulates NAM binding.

Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera Cheng

This study identifies molecular and genetic mechanisms underlying the transition from dioecy to monoecy in Diospyros oleifera using genome-wide analyses of 150 accessions.

Mechanosensitive channel-based optical membrane tension biosensor

The paper develops an optical biosensor to measure membrane tension by repurposing an E. coli mechanosensitive channel with circularly permuted GFP.

Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

The paper identifies and characterizes Caudoviricetes phages with genome terminal repeats in fecal metagenomes, finding 1,899 species-level units and 34 associations between phages and human phenotypes.

Nardilysin-Regulated Scission Mechanism Activates Polo-like Kinase 3 to Suppress the Development of Pancreatic Cancer

The paper identifies a post-translational mechanism where Nardilysin cleaves Plk3 to generate an active form that suppresses pancreatic cancer development and metastasis.

Predicting neoadjuvant chemotherapy benefit using deep learning from stromal histology in breast cancer

This study uses deep learning to predict neoadjuvant chemotherapy benefit in breast cancer using stromal histology, introducing the TS-score which outperforms existing predictors.

The faecal metabolome and its determinants in inflammatory bowel disease

This study identifies metabolic alterations in IBD patients by analyzing faecal metabolites, metagenomics, host genetics, and clinical data, finding over 300 differentially abundant molecules and associations with microbiota and diet.

HIV-linked gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV

This study links HIV-associated gut dysbiosis to cytokine production capacity in ART-suppressed PLHIV, identifying specific microbial strains associated with immune markers.

Strain dependent structural effects and in vivo efficacy of enterovirus-D68 inhibitors

This study develops a potent EV-D68 inhibitor, 11526092, showing improved in vitro potency and in vivo efficacy compared to pleconaril, with strain-dependent structural effects observed via cryo-EM.

Genetic, parental and lifestyle factors influence telomere length

This study identifies factors influencing telomere length across blood cell types, showing genetic, parental, and lifestyle effects, with maternal age's impact mediated by epigenetics.

In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing

This study identifies distinct antibody epitope repertoires in IBD patients using PhIP-seq, revealing differentially abundant antibodies associated with disease subtypes and features.

Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire

This study uses PhIP-Seq to analyze antibody repertoires in 1,443 individuals, showing genetic and environmental factors influence antibody diversity and phenotype associations.