Biology subjects

Gentry, E. C.

Publications and source records attributed to Gentry, E. C..

9 recordsLinked to original sources

bioRxiv2026

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.

bioinformatics↗

bioRxiv2024

Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus

Huanglongbing (HLB), associated with the psyllid-vectored phloem-limited bacterium, Candidatus Liberibacter asiaticus (CLas), is a disease threat to all citrus production worldwide. Currently, there are no sustainable curative or prophylactic treatments available. In this study, we utilized mass spectrometry (MS)-based metabolomics in combination with 3D molecular mapping to visualize complex chemistries within plant tissues to explore how these chemistries change in vivo in HLB-impacted trees. We demonstrate how spatial information from molecular maps of branches and single leaves yields insight into the biology not accessible otherwise. In particular, we found evidence that flavonoid biosynthesis is disrupted in HLB-impacted trees, and an increase in the polyamine, feruloylputrescine, is highly correlated with an increase in disease severity. Based on mechanistic details revealed by these molecular maps, followed by metabolic modeling, we formulated and tested the hypothesis that CLas infection either directly or indirectly converts the precursor compound, ferulic acid, to feruloylputrescine to suppress the antimicrobial effects of ferulic acid and biosynthetically downstream flavonoids. Using in vitro bioassays, we demonstrated that ferulic acid and bioflavonoids are indeed highly bactericidal to CLas, with the activity on par with a reference antibiotic, oxytetracycline, recently approved for HLB management. We propose these compounds should be evaluated as therapeutics alternatives to the antibiotics for HLB treatment. Overall, the utilized 3D metabolic mapping approach provides a promising methodological framework to identify pathogen-specific inhibitory compounds in planta for potential prophylactic or therapeutic applications.

plant biology↗

bioRxiv2023

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health.

microbiology↗

bioRxiv2022

Distinct bile salt hydrolase substrate preferences dictate C. difficile pathogenesis

Summary paragraphBile acids (BAs) mediate the crosstalk between human and microbial cells and influence intestinal diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate preferences and impact on C. difficile remain elusive. Here, we survey the diversity of Lactobacillus BSHs and unravel the structural basis of their substrate preference. We show that leveraging BSH activity and specificity is an effective strategy to prevent C. difficile growth in clinically relevant CDI models. A range of non-canonical conjugated BAs is also identified, comprising unique BSH substrates that also inhibit C. difficile spore germination. These findings establish BSHs as intestinal enzymes essential to BA homeostasis and colonization resistance against C. difficile. One sentence summaryBile salt hydrolase activity inhibits C. difficile by shaping the conventional and non-canonical conjugated bile acid pools

microbiology↗

bioRxiv2021

Non-Invasive Skin Sampling Detects Systemically Administered Drugs in Humans

Clinical testing typically relies on invasive blood draws and biopsies. Alternative methods of sample collection are continually being developed to improve patient experience; swabbing the skin is one of the least invasive sampling methods possible. To show that skin swabs in combination with untargeted mass spectrometry (metabolomics) can be used for non-invasive monitoring of an oral drug, we report the kinetics and metabolism of diphenhydramine in healthy volunteers (n=10) over the course of 24 hours in blood and three regions of the skin. Diphenhydramine and its metabolites were observed on the skin after peak plasma levels, varying by compound and skin location, and is an illustrative example of how systemically administered molecules can be detected on the skin surface. The observation of diphenhydramine directly from the skin supports the hypothesis that both parent drug and metabolites can be qualitatively measured from a simple non-invasive swab of the skin surface. The mechanism of the drug and metabolites pathway to the skins surface remains unknown.

pharmacology and toxicology↗

bioRxiv2021

Assigning confidence to structural annotations from mass spectra with COSMIC

Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but these libraries are vastly incomplete; in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. As biological interpretation relies on accurate structure annotations, the ability to assign confidence to such annotations is a key outstanding problem. We introduce the COSMIC workflow that combines structure database generation, in silico annotation, and a confidence score consisting of kernel density p-value estimation and a Support Vector Machine with enforced directionality of features. In evaluation, COSMIC annotates a substantial number of hits at small false discovery rates, and outperforms spectral library search for this purpose. To demonstrate that COSMIC can annotate structures never reported before, we annotated twelve novel bile acid conjugates; nine structures were confirmed by manual evaluation and two structures using synthetic standards. Second, we annotated and manually evaluated 315 molecular structures in human samples currently absent from the Human Metabolome Database. Third, we applied COSMIC to 17,400 experimental runs and annotated 1,715 structures with high confidence that were absent from spectral libraries.

bioinformatics↗

bioRxiv2020

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

bioinformatics↗

bioRxiv2019

Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure

RationaleA major hurdle in identifying chemicals in mass spectrometry experiments is the availability of MS/MS reference spectra in public databases. Currently, scientists purchase databases or use public databases such as GNPS. The MSMS-Chooser workflow empowers the creation of MS/MS reference spectra directly in the GNPS infrastructure.\n\nMethodsAn MSMS-Chooser sample template was completed with the required information and sequence tables were generated programmatically. Standards in methanol-water (1:1) solution (1 M) were placed into wells individually. An LC-MS/MS system using data-dependent acquisition in positive and negative modes was used. Species that may be generated under typical ESI conditions are chosen. The MS/MS spectra and MSMS-Chooser sample template were subsequently uploaded to MSMS-Chooser in GNPS for automatic MS/MS spectral annotation.\n\nResultsData acquisition quickly and effectively collected MS/MS spectra. MSMS-Chooser was able to accurately annotate 99.2% of the manually validated MS/MS scans that were generated from the chemical standards. The output of MSMS-Chooser includes a table ready for inclusion in the GNPS library (after inspection) as well as the ability to directly launch searches via MASST. Altogether, the data acquisition, processing, and upload to GNPS took ~2 hours for our proof-of-concept results.\n\nConclusionsThe MSMS-Chooser workflow enables the rapid data acquisition, analysis, and annotation of chemical standards, and uploads the MS/MS spectra to community-driven GNPS. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

bioinformatics↗

bioRxiv2019

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

bioinformatics↗