Biology subjects

Phelan, V. V.

Publications and source records attributed to Phelan, V. V..

5 recordsLinked to original sources

bioRxiv2023

Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits

Pseudomonas aeruginosa is a ubiquitous gram-negative opportunistic pathogen with remarkable phylogenetic and phenotypic variability. In this work, we applied classical molecular networking analysis to secondary metabolite profiling data from seven Pseudomonas aeruginosa strains, including five clinical isolates from the lung secretions of people with cystic fibrosis. Combined with whole-genome sequencing, we show that some P. aeruginosa isolates, including nmFLRO1, produce a previously unreported class of acyl putrescines, isolate SH3A does not produce di-rhamnolipids because its genome belongs to phylogenetic clade 5, and the secondary metabolite profile of isolate SH1B reflects a frame-shift mutation in the quorum sensing regulator rhlR. This study highlights for the first time that secondary metabolite profiling provides unique insight into genetic variation of P. aeruginosa. ImportanceSecondary metabolite profiling of Pseudomonas aeruginosa isolates can be used to identify rare genomic variants that impact quorum sensing and metabolite biosynthesis that underlie virulence.

microbiology↗

bioRxiv2022

A Universal Language for Finding Mass Spectrometry Data Patterns

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.

bioinformatics↗

bioRxiv2022

Pyochelin biotransformation shapes bacterial competition

Pseudomonas aeruginosa and Staphylococcus aureus are among the most frequently isolated bacterial species from polymicrobial infections of cystic fibrosis patients and chronic wounds. We applied mass spectrometry guided interaction studies to determine how chemical interaction shapes the fitness and community structure during co-infection of these two pathogens. We demonstrate that S. aureus is equipped with an elegant mechanism to inactivate pyochelin via the yet uncharacterized methyltransferase Spm (staphylococcal pyochelin methyltransferase). Methylation of pyochelin abolishes the siderophore activity of pyochelin and significantly lowers pyochelin-mediated intracellular ROS production in S. aureus. In a murine wound co-infection model, a S. aureus mutant unable to methylate pyochelin shows significantly lower fitness as compared to its parental strain. Thus, Spm mediated pyochelin methylation is a novel mechanism to increase S. aureus survival during in vivo competition with P. aeruginosa.

microbiology↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗

bioRxiv2021

Artificial Sputum Medium Formulation Impacts Pseudomonas aeruginosa Phenotype and Chemotype

Site-specific in vitro culture media are being developed to investigate microbial pathogenicity and ecology in nutrient environments that are more reflective of disease. For microbial ecology research in cystic fibrosis (CF), different artificial sputum media (ASM) formulations have been created to recapitulate the nutrient availability of the CF lung environment. However, these ASM formulations vary in concentration of amino acids, mucin, and other niche-specific compounds. Here, we measured the differential production of small molecule virulence factors by Pseudomonas aeruginosa, the predominant pathogen in CF pulmonary infections, cultured in nine different ASM formulations via liquid chromatography tandem mass spectrometry (LC-MS/MS) and molecular networking. We show that different ASM formulations lead to different phenotypes and metabolic profiles of P. aeruginosa and commercial porcine gastric mucin (PGM) contains a myriad of contaminants, including iron, which affect P. aeruginosa physiology. IMPORTANCEDifferent media formulations aiming to replicate in vivo infection environments contain different nutrients, which affects interpretation of experimental results. Inclusion of undefined components, such as commercial porcine gastric mucin (PGM), in an otherwise chemically defined medium can alter the nutrient content of the medium in unexpected ways and influence experimental outcomes.

microbiology↗