Biology subjects

Sturla, S.

Publications and source records attributed to Sturla, S..

4 recordsLinked to original sources

bioRxiv2026

Chemical probes reveal individualized gut microbiome biotransformation capacity and the impacts of ex vivo fermentation conditions

The gut microbiome transforms endogenous and exogenous chemicals, contributing to bioactivation or detoxification via the formation of metabolites with altered bioactivity. Most high content microbiome assays infer function from genetic composition rather than direct assessment of biotransformation activity, and it remains difficult to predict functional consequences of environmental factors and experimental variation. Therefore, we developed an anaerobic fecal fermentation workflow that couples targeted LC-MS/MS quantification of dynamic profiles of 20 chemical probes with untargeted metabolomics to profile human microbiome biotransformation capacity and used it to assess the impact of experimental conditions on biotransformation profiles. Across five donors and 240 fermentations, inoculum density and growth medium composition strongly influenced probe transformation rates, whereas the biotransformation capacities of fecal slurries frozen at -80{degrees}C did not differ from fresh fecal samples. Individual donors could be uniquely stratified on the basis of biotransformation profile data in a way that was not recapitulated by 16S rRNA taxonomic structure or predicted functional pathways. Finally, expected biotransformation products and metabolic trends could be confirmed with untargeted metabolomics characterization. This scalable platform directly profiles gut microbial biotransformation activity, supporting wider applications of standardized microbiome functional phenotyping in humans and quantitative models of microbiome-competent biokinetics assessment in pharmacology and toxicology.

microbiology↗

bioRxiv2025

Genome-wide mapping of 5'-aldehyde terminus induced by reactive oxygen species

DNA single strand breaks (SSBs) are abundant lesions due to cell metabolism and reactive oxygen species (ROS) and can lead to replication folk collapse, double strand break formation, genome rearrangements, cell death and disease. Among numerous chemical forms of SSBs, 5'-aldehyde terminus are the most abundant generated by hydroxyl radicals and pose significant challenge for cellular repair machinery due to the lack of specific end processing process, potentially leading to more severe biological consequences than other readily repairable SSBs. Herein we developed a new strategy to locate 5'-aldehyde terminus in genomic DNA at single-nucleotide resolution. The principle involves labelling the 5'-aldehyde terminus with an aminooxy-functionalized oligonucleotide, giving rise to a biocompatible altered DNA linkage and allowing labelled sites to be amplified by polymerase chain reaction. We sequenced the 5'-aldehyde terminus distribution in genomic DNA, nuclei, and cells following activation of the Fenton reaction. The results revealed a significant preference for adenine bases in DNA lesions and provided insights into the genome-wide distribution of such DNA damage, correlating with genomic features and chromatin accessibility. This method provide a new strategy for studies aiming to understand the biological and toxicological impacts of 5'-aldehyde termini in DNA as the form species of single strand break induced by reactive oxygen species from a human genome.

genomics↗

bioRxiv2024

Predicting in vivo concentrations of dietary hop phytoestrogens by physiologically based kinetic modeling

Hop extracts containing prenylated polyphenols such as 8-prenylnaringenin (8-PN) and its precursor isoxanthohumol (iXN) are popular among women seeking natural alternatives to hormone therapy for postmenopausal symptoms. Due to structural similarities with estrogens, these compounds act as estrogen receptor agonists. Especially 8-PN, described as the most potent phytoestrogen known to date, poses a potential risk for endocrine disruption. Therefore, its use as a hormone replacement raises concerns for human health. However, a significant challenge in assessing the potential endocrine-disruptive effects of hop polyphenols is the lack of data on their toxicokinetics. Particularly, information on in vivo concentrations in target tissues is lacking. To address this gap, we developed a physiologically based kinetic (PBK) model tailored to female physiology. The model was used to predict the levels of hop polyphenols in human blood and target tissues under realistic exposure scenarios. The predictions suggest that iXN and 8-PN concentrations in target tissues reach the low nanomolar range after dietary supplementation. This study enhances our understanding of the safety profile of hop polyphenols and highlights the need for further research into their use as an alternative to hormone therapy in menopausal women.

pharmacology and toxicology↗

bioRxiv2023

Catalytic and non-catalytic functions of DNA polymerase kappa in translesion DNA synthesis

Translesion DNA synthesis (TLS) is an essential process that allows cells to bypass lesions encountered during DNA replication and is emerging as a primary target of chemotherapy. Among vertebrate DNA polymerases, polymerase kappa (Pol() has the unique ability to bypass minor groove DNA adducts in vitro. However, Pol(is also required for cells to overcome major groove DNA adducts but the basis of this requirement is unclear. Here, we combine CRISPR base editor screening technology in human cells with TLS analysis of defined DNA lesions in Xenopus egg extracts to unravel the functions and regulations of Pol(during lesion bypass. Strikingly, we show that Pol(has two main functions during TLS, which are differentially regulated via Rev1 binding. On the one hand, Pol(is essential to replicate across minor groove DNA lesions in a process that depends on PCNA ubiquitylation but is independent of Rev1. On the other hand, via its cooperative interaction with Rev1 and ubiquitylated PCNA, Pol(stabilizes the Rev1-Pol(extension complex on DNA to allow extension past major groove DNA lesions and abasic sites, in a process that is independent of Pol(catalytic activity. Together, our work identifies catalytic and non-catalytic functions of Pol(in TLS and reveals important regulatory mechanisms underlying the unique domain architecture present at the C-terminal end of Y-family TLS polymerases.

molecular biology↗