Biology subjects

Vilchez-Larrea, S. C.

Publications and source records attributed to Vilchez-Larrea, S. C..

2 recordsLinked to original sources

bioRxiv2026

H3K4me3 exhibits length-dependent deposition patterns at transcription initiation regions in Trypanosoma cruzi and correlates with transcriptional activity

In trypanosmatids genes, transcribed by RNA polymerase II do not have canonical promoters and are organized into directional gene clusters that mature into monocistronic transcripts by a co-transcriptional process known as trans-splicing. Even though gene expression is regulated mainly post-transcriptionally, it is currently understood that chromatin and epigenetics are also involved in this regulation. In eukaryotes, specific signals are normally required for the occurrence of an appropriate transcription initiation. Among them, trimethylation of histone H3 in lysine 4 is the most conserved signal normally detected at transcription start sites of actively transcribed genes. Unlike many model organisms, trypanosomes do not have defined promoters. Instead, transcription initiates in a bidirectional manner from dispersed regions coincident with divergent strand switch regions located between directional gene clusters (DGCs). In T. cruzi, H3K4me3 was observed at the origins of transcription coincident with divergent strand switch regions (dSSRs) in epimastigotes, but it has not been mapped throughout the whole genome at base-pair resolution or in other life stages so far. Here, we set up the CUT&RUN technique for T. cruzi epimastigotes and trypomastigotes. Consistent with a predominant post-transcriptional regulation along the life cycle, we did not find significant differences between life stages. We corroborated that H3K4me3 is enriched at dSSR adjacent to actively expressed DGCs. Moreover, we noticed that this histone mark exhibits different patterns that correlate with the genomic span of the transcription initiation regions and with transcriptional activity. Furthermore, we unveiled that the most actively transcribed DGCs are associated with shorter dSSRs and are located within the core compartment of the genome displaying a more accessible chromatin.

genomics↗

bioRxiv2026

NN-Assisted Image Analysis for Quantifying Intracellular Trypanosoma cruzi Infection

Quantification of intracellular Trypanosoma cruzi infection remains a central, yet methodologically challenging step in Chagas disease research and early-stage drug discovery. Current approaches largely rely on manual microscopy-based counting or on genetically modified parasites, both of which present limitations in scalability, reproducibility, or accessibility. Here, we developed and validated a neural network (NN)-based pipeline for the automated quantification of infection rates and parasite burden in mammalian cells using images stained exclusively with DNA-binding fluorescent dyes. Two independently refined deep-learning models were trained to segment host cell nuclei and intracellular amastigotes, respectively, and subsequently integrated into a unified algorithm that assigns each parasite to its nearest host cell. The pipeline was evaluated using confocal images from six mammalian cell lines infected with two T. cruzi strains and compared against blinded manual quantification. Automated detection of both, host nuclei and parasites, showed high concordance with manual counts, with median deviations around 5% and similar distributions of parasite burden per cell. In contrast to morphology-based image analysis methods, our NN-based approach demonstrated improved robustness across diverse cell types and staining conditions, reduced parameter dependency, and independent segmentation of host and parasite objects, minimizing error propagation. Although minor biases in parasite-to-cell assignment were observed in densely clustered cultures, overall infection indexes and burden estimates closely matched manual analysis. This accessible and scalable AI-assisted workflow provides a reproducible alternative to manual quantification and represents a methodological advance for standardized phenotypic screening of intracellular T. cruzi, supporting more robust and harmonized drug discovery efforts in Chagas disease.

microbiology↗