Biology subjects

Yamaguchi, L. F.

Publications and source records attributed to Yamaguchi, L. F..

3 recordsLinked to original sources

bioRxiv2026

Siderophore identification in microorganisms associated with marine sponges by LC-HRMS and a data analytic approach in R.

Siderophores are pivotal iron-acquisition biomolecules integral to microbial survival, pathogenicity, and ecology. Elucidating these compounds offers critical insights into the microbial dynamics of marine holobionts and potential therapeutic applications. In this study, we present a culture-independent, data-centric strategy to identify siderophores from the microbiome of three marine sponge species: Dragmacidon reticulatum, Aplysina fulva, and Amphimedon viridis. Utilizing Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) coupled with a custom R-based analytical workflow (XCMS and MetaboAnnotation), we successfully annotated 59 potential siderophores, 41 of which were confirmed via chromatographic profiling. We employed a rigorous validation pipeline, utilizing multiple iron-adduct calculations [M-2H+Fe]+, [M-H+Fe]2+, [2M-2H+Fe]+, high mass accuracy thresholds (<3 ppm), and retention time precision (CV < 2%). Notably, iron supplementation during extraction did not significantly alter siderophore detection, suggesting constitutive production or environmental saturation. This workflow bypasses the limitations of traditional cultivation, revealing a diverse landscape of iron-chelating metabolites--including Ferricrocin, Aeruginic acid, and Madurastatin--directly within the sponge holobiont.

bioinformatics↗

bioRxiv2020

Evidence for both phylogenetic conservatism and lability in the evolution of secondary chemistry in a tropical angiosperm radiation

Over evolutionary timescales, shifts in plant secondary chemistry may be associated with patterns of diversification in associated arthropods. Although foundational hypotheses of plant-insect codiversification and plant defense theory posit closely related plants should have similar chemical profiles, numerous studies have documented variation in the degree of phylogenetic signal, suggesting phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and genotyping-by-sequencing to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Broad metabolite classes displayed strong phylogenetic signal, whereas the crude 1H NMR spectra featured evolutionary lability in chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the others state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of broad compound classes and concomitant evolutionary lability of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

evolutionary biology↗

bioRxiv2018

Description and charactrization of the Amazonian entomopathogenic bacterium Photorhabdus luminescens MN7

Many isolates of the genus Photorhabdus have been reported around the world. Here we describe the first Brazilian Photorhabdus isolate, found in association with the entomopathogenic nematode Heterorhabditis baujardi LPP7, from the Amazonian forest in Monte Negro (RO, Brazil). The new isolate can be grouped with the Hb-Hm clade of P. luminescens subsp. luminescens, close to the new subspecies P. luminescens subsp. sonorensis. P. luminescens MN7 has several characteristics expected of variant form I cells, such as the presence of intracellular crystals, secretion of hydrolytic enzymes (lipases and proteases) and bioluminescence. Although H. baujardi LPP7 is not prolific when compared to H. bacteriophora HP88, P. luminescens MN7 is clearly pathogenic and probably secretes the same toxins as P. luminescens subsp. luminescens W14, when fed to larvae of the greater wax moth Galleria mellonella. This behavior is different from what is found in Photorhabdus luminescens subsp. laumondii HP88, which was used as a control in our experiments, and P. l. subsp. laumondii TT01. Besides the toxin secretion, P. luminescens MN7 secretes proteolytic polypeptides that have molecular masses different from those found in P. l. subsp. laumondii TT01. Finally, the crude extract from spent culture medium was shown to contain 3,5-dihydroxy-4-isopropyl-cis-stilbene and 1,3,8-trihydroxy-9,10-anthraquinone as the major compounds, similarly to other Photorhabdus luminescens strains.

microbiology↗