Biology subjects

Cooperstone, J.

Publications and source records attributed to Cooperstone, J..

3 recordsLinked to original sources

bioRxiv2025

MS2extract: an R Package for a Scalable LC-MS/MS Library Creation

Reference MS/MS libraries are useful to aid in metabolomics compound identification. However, creating these libraries can be challenging because of the complexity of MS/MS data handling, the need for manual spectrum inspection, and requirement for custom-designed bioinformatics tools for this purpose. Although licensed and open-source alternatives to create MS/MS reference libraries exist, most of these pipelines require manual extraction of each reference spectrum, which is a time-consuming and error-prone process. Here, we present MS2extract, an R package facilitating the user-led creation and automation of MS/MS spectral libraries. The core MS2extract workflow consists of importing MS/MS raw data, detecting specific precursor ions, extracting MS/MS spectra, removing low-intensity signals, and exporting a spectral database. In addition, libraries created with MS2extract are compatible with GNPS2 batch upload to maximize MS/MS library reuse. We used MS2extract to create PhenolicsDB, a phenolics-focused MS/MS library with fragmentation patterns of 71 authentic analytical standards collected in positive and negative polarity, and multiple collision energies, with 320 MS/MS reference spectra. Finally, we employed PhenolicsDB to identify apple fruit phenolics. MS2extract and PhenolicsDB are free and publicly available for download and use, and PhenolicsDB is also available in GNPS2.

bioinformatics↗

bioRxiv2024

Discovery of steroidal alkaloid metabolites and their accumulation in pigs after short-term tomato consumption

ScopeWhole tomato consumption has been shown to be more effective than lycopene alone against chronic disease risks, suggesting other phytochemicals play a role in the health properties of tomato-rich diets. Recently, metabolites of tomato steroidal alkaloids, an understudied class of secondary plant compounds, have been found in plasma, tissues, and urine. However, a comprehensive, targeted analysis to determine which steroidal alkaloid metabolites are present after tomato consumption is lacking. This study profiles and quantifies tomato steroidal alkaloids in blood for the first time. Methods and resultsIn a two-week parallel-arm study, piglets (n = 20) were fed diets containing 10% tomato powder or a macronutrient-matched control. Steroidal alkaloids were extracted from plasma and quantified using LC-MS. Tomatidine and alpha-tomatine were detected in plasma and confirmed with standards, while mass fragmentation spectra aided in identifying 31 additional metabolites representing 9 unique masses. Concentrations averaged to 107.7 nmol/L plasma, comprising of phase I (66%) and phase II (4.5%) metabolites. ConclusionThese results describe the profile and concentration of steroidal alkaloid metabolites in pig plasma after short-term tomato consumption. Our methodology and findings allow for future investigations of tomato steroidal alkaloid bioactivity using physiologically appropriate levels.

pharmacology and toxicology↗

bioRxiv2021

Solanum galapagense-derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

One hypothesis for the origin of endemic species of tomato on the Galapagos islands postulates a hybridization of Solanum pimpinellifolium and S. habrochaites. S. galapagense accession LA1141 has purple fruit pigmentation which has previously been described in green-fruited wild tomatoes such as S. habrochaites. Characterization of LA1141 derived purple pigmentation provides a test of the hybridization hypothesis. Purple pigmentation was recovered in progenies derived from LA1141 and the anthocyanins malvidin 3(coumaroyl)rutinoside-5-glucoside, petunidin 3-(coumaroyl) rutinoside-5-glucoside, and petunidin 3-(caffeoyl)rutinoside-5-glucoside were abundant. Fruit color was evaluated in an introgression population and three quantitative trait loci (QTLs) were mapped and validated in subsequent populations. The loci atroviolacium on chromosome 7, Anthocyanin fruit on chromosome 10, and uniform ripening also on chromosome 10, underly these QTLs. Sequence analysis suggested that the LA1141 alleles of Aft and atv are unique relative to those previously described from S. chilense accession LA0458 and S. cheesmaniae accession LA0434, respectively. Phylogenetic analysis of the LA1141 Aft genomic sequence did not support a green-fruited origin and the locus clustered with members of the red-fruited tomato clade. The LA1141 allele of Aft is not the result of an ancient introgression and underlies a gain of anthocyanin pigmentation in the red-fruited clade. HighlightAnthocyanin fruit and atroviolacium confer purple pigmentation in Solanum galapagense LA1141 confirming a mechanism described for green-fruited tomatoes. LA1141 alleles cluster with red-fruited homologs suggesting an independent gain of pigmentation.

plant biology↗