Kiran Raosaheb Patil

YBX3 overexpression in mesothelioma drives aberrant cell proliferation

This study identifies YBX3 as an oncoprotein in mesothelioma that drives cell proliferation through SLC7A5/LAT1-mediated amino acid uptake and shows JPH203 as a potential therapeutic agent.

Obligate cross-feeding of metabolites is common in soil microbial communities

The paper shows that many soil bacteria depend on metabolite supplementation from other community members, revealing widespread cross-feeding in soil microbial communities.

Network-scale disruption of RNA-protein interactions by a bioaccumulating small-molecule drug

This study shows that the antidepressant duloxetine disrupts RNA-protein interactions in both human and bacterial cells, revealing a new mechanism of drug action.

Laboratory evolution enhances resilience of a symbiont yeast and its honeybee host against agrochemical exposure

The paper uses laboratory evolution to identify yeast resistance mechanisms against agrochemicals and shows how evolved yeast can protect honeybee hosts.

CarveMe-GutMicrobes: Automated Metabolic Model Reconstruction for Gut Microbial Species and Communities

CarveMe-GutMicrobes reconstructs genome-scale metabolic models for gut microbes from genomic data, showing high accuracy in predicting gene essentiality and metabolite secretion.

Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics

This study investigates interactions between low-calorie sweeteners and xenobiotics on gut bacteria, finding synergistic effects that alter bacterial growth and host cell responses.

Oxygen gradients reshape cross-feeding through emergent spatial organization of gut commensal bacteria

The paper shows how oxygen gradients in the gut reshape cross-feeding between Bacteroides thetaiotaomicron and Escherichia coli through spatial organization and metabolic feedback.

Off-purpose activity of industrial and agricultural chemicals against human gut bacteria

This study investigates the off-target antibacterial effects of 1076 industrial and agricultural chemicals on 22 human gut bacteria, revealing 588 previously unreported interactions.

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales

The paper develops tools for transposon mutagenesis in Bacteroidales to identify essential genes and functional elements across three gut bacteria.

Bacteroides-driven metabolic remodelling suppresses Clostridioides difficile toxin expression in mixed biofilm communities

This study shows Bacteroides species inhibit C. difficile toxin production through cross-feeding proline in mixed biofilms, revealing a mechanism for microbiota-mediated control of CDI.

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

This paper combines cryo-EM and FIB-SIMS to map sub-cellular chemical distributions in bacteria, revealing pollutant storage in phase-separated aggregates.

Extensive PFAS accumulation by human gut bacteria

This study shows human gut bacteria can accumulate PFAS, with some species like Bacteroides uniformis accumulating them to high concentrations, and identifies mechanisms involving transmembrane transport and efflux pumps.

Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism

This study examines how bacterial proteomes and metabolomes change in response to interspecies interactions in gut microbiota co-cultures, revealing extensive molecular reorganization and emergent metabolic pathways.

Metabolic control of germ layer proportions through regulation of Nodal and Wnt signalling

The paper shows that glycolytic activity regulates germ layer proportions by modulating Nodal and Wnt signalling in mouse gastrulation.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Emergent metabolic interactions in resistance to Clostridioides difficile invasion

The paper identifies key microbial interactions and metabolic pathways that confer resistance to C. difficile invasion using synthetic and clinical communities.

Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes

This study develops a parallelized ALE platform to evolve wine yeasts with enhanced metabolic traits, finding that expanded replicates and lineages improve the chances of evolving improved strains with desirable industrial performance.

Emergent survival and extinction of species within gut bacterial communities

The paper shows how species in gut bacterial communities can survive or go extinct based on resource availability and metabolic interactions, identifying emergent survival and community-driven extinctions.

Glycolytic flux-signaling controls mouse embryo mesoderm development

The paper shows that FBP, a glycolytic metabolite, affects mesoderm segmentation in mouse embryos by altering subcellular protein localization and Wnt-signaling.

Operation of a TCA cycle subnetwork in the mammalian nucleus

The paper shows that parts of the TCA cycle operate in the nucleus, challenging the canonical view of metabolic compartmentalization.

A genome-scale metabolic model of Drosophila melanogaster for integrative analysis of brain diseases

The paper develops a genome-scale metabolic model for Drosophila melanogaster to study metabolic disorders and Parkinson's disease.

RNA regulates Glycolysis and Embryonic Stem Cell Differentiation via Enolase 1

The paper shows RNA regulates ENO1 enzyme activity, affecting glycolysis and stem cell differentiation in human and mouse cells.

Co-translational assembly counteracts promiscuous interactions

The paper identifies co-translational assembly domains in proteins that facilitate interactions between nascent chains and fully synthesized subunits, revealing their role in regulating complex assembly pathways.

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.

metaGEM reconstructs genome-scale metabolic models directly from metagenomes, demonstrating comparable metabolic representation to reference-based models and capturing intraspecies diversity in gut microbiomes.

Predictive evolution of metabolic phenotypes using model-designed selection niches

This paper predicts the evolution of fitness-costly traits by designing selection niches using metabolic models and validates it in yeast for increased aroma compound secretion.

Bioactivity assessment of natural compounds using machine learning models based on drug target similarity

This paper develops a machine learning model to predict protein targets of natural compounds based on drug target similarity, identifying potential therapeutics with experimental validation.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development

The paper identifies CD44 as a marker and regulator of haematopoietic stem cell development through single-cell transcriptomics and functional experiments.

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

CarveMe automates the reconstruction of genome-scale metabolic models for microbial species and communities, achieving performance comparable to manual curation.