metabolomics

Coarse-graining genome-scale metabolic models for dynamic, multi-scale simulations of Pseudomonas aeruginosa in gel environments

This paper introduces GEM-CM, a computational framework that couples reaction-diffusion models with genome-scale metabolic models to simulate Pseudomonas aeruginosa growth and pyocyanin production in agar gels.

Evaluating non-oxidative glycolysis using 13C metabolic flux analysis

This study evaluates the precision of 13C metabolic flux analysis using different glucose tracers to estimate non-oxidative glycolysis fluxes in E. coli.

Gut Roseburia hominis-derived 10-hydroxystearic acid alleviates metabolic disorder by restoring hepatic fatty acid metabolism

This study identifies Roseburia hominis-derived 10-hydroxystearic acid as a metabolite that improves metabolic health by restoring hepatic fatty acid metabolism in mice.

A Urinary Metabolomic Signature Associated with Small Intestinal Bacterial Overgrowth in Children with Short Bowel Syndrome

The paper identifies a urinary metabolomic signature linked to small intestinal bacterial overgrowth in children with short bowel syndrome using gas chromatography/mass spectrometry.

Plant-plant communication in tomato: mechanisms underpinning information transfer between plants

This study investigates plant-plant communication in tomato by analyzing metabolomic and volatile emissions changes in response to herbivory, showing mirror effects in immune system reprogramming between sender and receiver plants.

Floral scent diversity and evolution in deceptive Cypripedium, and post-pollination effects on floral scent and its biosynthesis in C. henryi

This study characterizes floral scent diversity in Cypripedium orchids, finds high chemical diversity with weak phylogenetic signal, and shows limited post-pollination effects on scent composition and gene expression in C. henryi.

A Reproducible Pre-Transplant γδ T-cell Effector Signature Reveals Immune-Metabolic Programs Associated with Kidney Allograft Rejection

The paper identifies a pre-transplant γδ T-cell effector signature associated with kidney allograft rejection using multi-omics data from transplant recipients.

Resolving Gene-Metabolism Links through Multi-Metabolite mQTL Commonality Analysis

The paper develops a method to link genes to metabolism by analyzing commonality in metabolite features associated with mQTLs, demonstrating its effectiveness through three case studies.

Age-related biological dysregulation quantified using metabolomics is composed of distinct subsystems with synergistic associations to health outcomes: An analysis of the Canadian Longitudinal Study on Aging

The paper quantifies age-related biological dysregulation using metabolomics in older adults and shows it has distinct subsystems linked to health outcomes and DNA methylation.

Singular Value Decomposition for the Automated Analysis of NMR Fraction Libraries

This paper introduces an automated method using singular value decomposition to analyze NMR fraction libraries for molecular component identification and quantification.

Enzyme-Constrained Metabolic Modeling Reveals CO2-Dependent Growth Control in Picochlorum celeri

The paper uses enzyme-constrained metabolic modeling to show that Picochlorum celeri's rapid growth at elevated CO2 is due to protein budget allocation, not enzyme abundance.

Mapping bacterial bile amidation across the bile salt hydrolase family

The paper maps bacterial bile amidation by analyzing BSH transaminase activities and identifying BBAs in human samples.

Phloem conductance from leaf to fruits in avocado during development

The paper quantifies phloem conduit geometry and carbohydrate concentrations in avocado plants during development, showing changes in phloem structure and transport efficiency.

Plasma untargeted metabolomics reveals distinct metabolic disturbances between sexes following inhalation of ultrafine particles and exposure to aircraft noise in mice

This study uses metabolomics to show that UFP and aircraft noise exposure cause sex-specific metabolic changes in mice, with AN having the greatest impact and combined exposure showing sex-dependent effects.

Spatial and developmental reprogramming enables root growth under high salinity

This study identifies spatial developmental reprogramming in roots of Schrenkiella parvula under salinity, revealing distinct zones and regulatory programs that enable continued growth.

Integrative multi-omics re-analysis of public sequencing and metabolomics repositories defines the mucosal immune and metabolic landscape of Helicobacter pylori infection and supports CagW as a rational mRNA-LNP vaccine antigen

The paper re-analyses public multi-omics data to characterize the gastric mucosal immune and metabolic landscape of H. pylori infection and identifies CagW as a promising mRNA-LNP vaccine antigen.

Lipid Changes due to Low O-GlcNAc and the Downstream Consequences

This study investigates the effects of O-GlcNAc depletion on lipid metabolism and shows that it leads to lipid remodeling and increased sensitivity to ferroptosis.

Specialisation of photosynthetic biochemistry in C4 chloroplasts potentiates distinct cell-specific functionality of different chloroplast-to-nucleus retrograde signalling pathways.

The paper shows that chloroplast-to-nucleus retrograde signalling pathways are cell-specific in C4 plants, correlating with photosynthetic specialisation in mesophyll and bundle sheath cells.

Soft Sensing of Intracellular States for CHO Cell Bioprocessing with Ensemble Kalman Filters

This paper uses Ensemble Kalman Filters to estimate intracellular nucleotide sugar donors in CHO cell cultures from extracellular measurements, improving metabolic state inference.

Dietary fibre responses emerge through host-dietary regime interplay: Apple pectin modulates immune reactivity in adult zebrafish

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.

Integrative multi-omics decoding of the host response to Klebsiella pneumoniae infection reveals an itaconate-centred metabolic-immune axis and a spatially organised inflammatory programme

This study integrates multi-omics data from Kp infection to identify an itaconate-centred metabolic-immune axis and a host-response signature with high diagnostic accuracy.

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

An integrated identifiability and metabolic flux analysis workflow for reducing and repairing dynamic CHO metabolic models

The paper develops a workflow to reduce and repair dynamic metabolic models of CHO cells using identifiability analysis and metabolic flux analysis, improving prediction accuracy for specific growth rate and productivity.

Metabolism-Informed Bioreactor Model for Transferring Knowledge from Fed-batch to Continuous Biomanufacturing

This paper develops a metabolism-informed bioreactor model to transfer knowledge from fed-batch to continuous biomanufacturing by predicting intracellular fluxes and extracellular concentrations.

Integrated tissue proteomics and lipidomics from ovine organs suggests novel functional implications for fatty acids and lipid mediators.

The paper integrates proteomics and lipidomics data from sheep organs to functionally annotate lipid mediators and identify novel roles for fatty acids in protein synthesis and inflammation resolution.

Metabolic landscape of inborn errors of metabolism

This study uses metabolomics to analyze 474 subjects with inborn errors of metabolism, identifying genotype-specific metabolic alterations and providing diagnostic tools and a database of metabolomic features.

Multi-omics uncover interactions in the vaginal microbiome and a type II secretion/Tad pilus system in Gardnerella species

This study uses multi-omics to uncover Gardnerella genomic features linked to biofilm formation and interspecies interactions in the vaginal microbiome, identifying potential therapeutic targets for bacterial vaginosis.

Metabolic and transcriptional responses reveal co-option of symbiotic processes during early soybean-soybean cyst nematode interaction

This study identifies metabolic and transcriptional changes in soybean during soybean cyst nematode infection, revealing immune system remodeling and co-option of symbiotic processes.

Zea Lip: An atlas of glycerolipid profiles across leaf development in maize

UHPLC-MS/MS lipidomics of maize leaves (149 species, three genotypes, four growth stages, three leaf zones) shows genotype and leaf number explain most lipid variation.

Transcriptomic and metabolomic profiling reveals early responses of tomato plants elicited by compost-derived bacteria

This study examines the early molecular and metabolic responses of tomato plants to compost-derived bacteria, identifying common and strain-specific physiological signatures.