Z. Ning

Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry

This study evaluates how different experimental workflows affect fecal metaproteomic results, showing that DIA-PASEF improves protein identification and small protein recovery compared to DDA.

An R-R-type MYB transcription factor promotes nonclimacteric pepper fruit ripening pigmentation

This study identifies a MYB transcription factor that regulates capsanthin biosynthesis in nonclimacteric pepper fruit, showing its role in carotenoid accumulation and interaction with abscisic acid.

The evolution of two transmissible leukaemias colonizing the coasts of Europe

This study investigates the origin and evolution of two transmissible leukaemias in common cockles, identifying clonal origins, mutational signatures, and genomic instability.

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics

RapidAIM 2.0 evaluates gut microbiome functional responses to xenobiotics using high-throughput metaproteomics and in vitro culturing.

The evolution of two transmissible cancers in Tasmanian devils

This study analyzes the genetic diversity and evolution of two transmissible cancers in Tasmanian devils, revealing their emergence dates, mutation rates, and evolutionary patterns.

Gut microbiota-derived tryptamine impairs insulin sensitivity

This study identifies tryptamine, a gut microbiota-derived metabolite, as a contributor to insulin resistance in type 2 diabetes through TAAR1-ERK signaling.

Phenethylamine-producing gut bacteria induces diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis

This study identifies Ruminococcus gnavus as a gut bacterium that contributes to IBS-D by increasing serotonin biosynthesis through phenethylamine production.

Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome

This study evaluates the functional effects of 21 common sweeteners on human gut microbiomes using metaproteomics, identifying potential prebiotic properties in certain sugar alcohols.

A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago

The paper investigates the origin and function of the STORR gene fusion in Papaver species, finding it occurred once between 17-25 million years ago and is not exclusive to morphinan production.

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

This study evaluates the cultivability and functional activity of biobanked microbiota using an ex vivo assay and metaproteomics, showing stability after long-term freezing.

Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

This study evaluates the impact of BAFASAL, a bacteriophage preparation, on human gut microbiome composition and function using multi-omics analyses in an ex vivo setting.

Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 binding

Exploring the microbiome-wide lysine acetylation, succinylation and propionylation in human gut microbiota

The paper develops a method to analyze lysine acylations in the human gut microbiome, identifying thousands of modified peptides and showing differential distribution across microbial species.

An Antioxidant Enzyme Therapeutic for COVID-19

This paper describes a catalase-based therapeutic for COVID-19 that reduces oxidative stress and cytokine production in human and animal models without toxicity.

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics.

The paper develops a metaproteomic workflow and software tool to study gut microbiome functional dynamics using stable isotopic labeling and time series analysis.

Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak

The paper measures SARS-CoV-2 RNA concentration in aerosols from different areas of Wuhan hospitals during the COVID-19 outbreak and finds that aerosol transmission is possible under certain conditions.

Metaproteomic responses of in vitro gut microbiomes to resistant starches: the role of resistant starch type and inter-individual variations

This study examines how different types of resistant starches affect gut microbiome protein expression and functional pathways, revealing inter-individual variations in responses.

Growth phase-dependent responses of an in vitro gut microbiome to metformin

This study shows that metformin affects in vitro gut microbiota differently depending on when it is added during growth phases, with the log phase showing the strongest impact on growth and functional changes.

Aging immune system-related blood cell DNA methylation can predict the onset of early stage colorectal cancer

This study identifies DNA methylation of DZIP3 as a marker for early stage colorectal cancer, linked to aging and immune cell composition.

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

The paper develops an in vitro model called Mipro that maintains gut microbiome functional and compositional profiles, showing strong correlation with in vivo responses to metformin.

RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

RapidAIM screens xenobiotics against individual microbiomes using metaproteomics, showing compound effects on abundance, composition, and functional pathways across individuals.

A Clostridia-rich microbiota contributes to increased excretion of bile acids in diarrhea-predominant irritable bowel syndrome

This study identifies a Clostridia-rich microbiota as a contributor to excessive bile acid excretion in IBS-D patients through metagenomic and metabolomic analyses.

Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer's Disease Mouse Model

This study shows that inhibiting CK1δ/ε improves memory and circadian rhythms in Alzheimer's mice by reversing proteomic changes and synaptic plasticity.