Biology subjects

Perea, C.

Publications and source records attributed to Perea, C..

3 recordsLinked to original sources

bioRxiv2026

EpiFlow: multidimensional single-cell epigenetic profiling by spectral flow cytometry

The epigenetic landscape of individual cells determines their identity and function, yet current methods for profiling chromatin modifications at single-cell resolution remain low-throughput, costly, or limited in parametric depth. Here we present EpiFlow, a spectral flow cytometry-based platform that enables the simultaneous quantification of 16 epigenetic markers, including histone post-translational modifications, DNA methylation, and hydroxymethylation, at the single-cell level. We demonstrate that EpiFlow is robust across species from yeast to mammals and resolves biologically meaningful epigenetic transitions during the cell cycle, stem cell differentiation, germinal centre B cell maturation, diabetic liver remodelling, and seizure-induced chromatin reprogramming. High-dimensional integration of EpiFlow data enables cell-type classification based solely on epigenetic profiles in liver, brain, blood, and cancer. Furthermore, EpiFlow detects on-target and off-target/indirect effects of epigenetic drugs in a high-throughput-compatible format. Collectively, these results establish EpiFlow as a broadly applicable platform for single-cell epigenetic analysis in basic, pharmaceutical, and translational research.

cell biology↗

bioRxiv2025

Integrating image-based phenotyping and GWAS to map tolerance to Spittlebug nymphs in interspecific Urochloa grasses

Urochloa grasses are among the most widely used forage grasses across the tropics. Spittlebugs (Hemiptera: Cercopidae) are major pests of tropical Urochloa (syn. Brachiaria) pastures, severely reducing forage productivity and quality. Understanding the genetic basis of host-plant resistance is essential for developing durable resistant cultivars. Here, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of tolerance to Aeneolamia varia nymphs in 339 interspecific F hybrids derived from crosses between resistant sexual and susceptible apomictic Urochloa parents. Digital image analysis using both unsupervised (DQU) and supervised (DTR) quantification pipelines enabled precise estimation of plant damage, yielding moderate to high broad-sense heritability estimates (H{superscript 2} = 0.49-0.66). In contrast, insect survival (NTS) exhibited low to moderate correlations with all damage traits and lower heritability estimates (H{superscript 2} = 0.42). Using 57,051 high-quality SNPs aligned to the genome of the hybrid cultivar Basilisk, GWAS models identified 18 quantitative trait loci (QTL) for plant damage traits, but none for insect survival (antibiosis). Six robust QTL on chromosomes 1, 6, 7, 27, 29, and 36 were consistently detected across models and phenotyping methods, explaining up to 21.5% of phenotypic variance. Candidate gene analysis revealed proteins involved in hormone signalling, oxidative stress response, and cell wall modification, suggesting multifaceted tolerance mechanisms. These results provide a foundational set of molecular markers associated with spittlebug tolerance in Urochloa, useful for marker-assisted and genomic selection in our forage breeding programme.

plant biology↗

bioRxiv2024

Phylogenetic analysis of Mycobacterium bovis Reveals Evidence Of Animal And Zoonotic Tuberculosis Transmission Between Morocco And European Countries

Livestock production is a fundamental pillar of the Moroccan economy. Infectious diseases of cattle and other species represent a significant threat to the livestock industry, animal health, and food safety and security. Bovine tuberculosis (bTB), mainly caused by Mycobacterium bovis (M. bovis), generates considerable direct and indirect economic losses, in addition to the unknown human health burden caused by zoonotic transmission. Previous studies have suggested likely M. bovis transmission links between Morocco and Southern Europe, however, limitations inherent with the methods used prevented more definitive conclusions from being drawn. In this study, we employed whole genome sequencing analysis of a large set of M. bovis isolates to better define the phylogenetic links between strains from Morocco and neighboring countries. A total of 780 M. bovis sequences representing 36 countries were included in the study. The results of SNP analysis showed a close genetic relationship between M. bovis from Morocco and each of Spain, France, Portugal and Germany, this is supported by animal trade between Morocco and these countries, in addition to the important human migration from Morocco to Europe and North America. Regarding zoonotic tuberculosis (TB) transmission, we were able to find genetic links between M. bovis isolates from cattle in Morocco and humans in Italy, Germany, and the UK. These results support our hypothesis of significant transmission of M. bovis from cattle to humans, which calls for further investigations of zoonotic TB transmission in Morocco and in other countries. The fact that no M. bovis sequences from North Africa in the present database were classified as AF1 or AF2 clonal complexes suggests that the Sahara might play a role in preventing M. bovis transmission between North Africa and Sub-Saharan Africa. Our study benefits from a large sample size and a rich dataset that includes sequences from cattle, wildlife, and humans from Morocco and neighboring countries, enabling the delineation of M. bovis transmission routes within the animal-human interface.

molecular biology↗