Biology subjects

Robles, D.

Publications and source records attributed to Robles, D..

6 recordsLinked to original sources

bioRxiv2025

DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis

Genome regulation relies on complex and dynamic interactions between DNA and proteins. Recently, powerful methods have emerged that leverage third-generation sequencing to map protein-DNA interactions genome-wide. For example, Directed Methylation with Long-read sequencing (DiMeLo-seq) enables mapping of protein-DNA interactions along long, single chromatin fibers, including in highly repetitive genomic regions. However, DiMeLo-seq involves lossy centrifugation-based wash steps that limit its applicability to many sample types. To address this, we developed DiMeLo-cito, a single-tube, wash-free protocol that maximizes the yield and quality of genomic DNA obtained for long-read sequencing. This protocol enables the interrogation of genome-wide protein binding with as few as 100,000 cells and without the requirement of a nuclear envelope, enabling confident measurement of protein-DNA interactions during mitosis. Using this protocol, we detected strong binding of CTCF to mitotic chromosomes in diploid human cells, in contrast with earlier studies in karyotypically unstable cancer cell lines, suggesting that CTCF "bookmarks" specific sites critical for maintaining genome architecture across cell divisions. By expanding the capabilities of DiMeLo-seq to a broader range of sample types, DiMeLo-cito can provide new insights into genome regulation and organization.

genomics↗

bioRxiv2024

A Vector System Encoding Histone H3 Mutants Facilitates Manipulations of the Neuronal Epigenome

The differentiation of developmental cell lineages is associated with genome-wide modifications in histone H3 methylation. However, the causal role of histone H3 methylation in transcriptional regulation and cell differentiation has been difficult to test in mammals. The experimental overexpression of histone H3 mutants carrying lysine-to-methionine (K-to-M) substitutions has emerged as an alternative tool for inhibiting the endogenous levels of histone H3 methylation at specific lysine residues. Here, we leverage the use of histone K-to-M mutants by creating Enhanced Episomal Vectors that enable the simultaneous depletion of multiple levels of histone H3 lysine 4 (H3K4) or lysine 9 (H3K9) methylation in projection neurons of the mouse cerebral cortex. Our approach also facilitates the simultaneous depletion of H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3, respectively) in cortical neurons. In addition, we report a tamoxifen-inducible Cre-FLEX system that allows the activation of mutant histones at specific developmental time points or in the adult cortex, leading to the depletion of specific histone marks. The tools presented here can be implemented in other experimental systems, such as human in vitro models, to test the combinatorial role of histone methylations in developmental fate decisions and the maintenance of cell identity.

neuroscience↗

bioRxiv2022

Surrounding Traffic Matters: Increases in Traffic Volume Are Related to Changes in EEG Rhythms in Urban Cyclists.

In this study, we used an oddball EEG bicycle paradigm to study how changes in urban environments elicit changes in EEG markers. Participants completed an auditory oddball task while riding in three different cycling lane environments. A low traffic condition where participants rode in a fully separated bike lane alongside a quiet residential street, an intermediate traffic condition where participants rode alongside a busy residential street in a painted lane, and a heavy traffic condition where participants rode alongside fast/heavy traffic on a shared-use path. Relative to the low traffic, heavy traffic was associated with faster reaction time and a trend towards reduced accuracy, and increased N1 amplitude evoked by the standard tones. We attribute this difference in N1 amplitude to different attentional demands evoked by the different traffic conditions. In this fashion, heavy traffic requires greater auditory filtering. Furthermore, we found no differences in P3 amplitude associated with the traffic conditions. We discuss the implications of mobile paradigms to study attention in real-world settings.

neuroscience↗

bioRxiv2021

Xenotransplantation of porcine progenitor cells in an epileptic California sea lion (Zalophus californianus)

BackgroundDomoic acid (DA) is a naturally occurring neurotoxin harmful to marine animals and humans. California sea lions exposed to DA in prey during algal blooms along the Pacific coast exhibit significant neurological symptoms, including epilepsy with hippocampal atrophy. ObservationsHere we describe a xenotransplantation procedure to deliver interneuron progenitor cells into the damaged hippocampus of an epileptic sea lion with suspected DA toxicosis. The sea lion has had no evidence of seizures following the procedure, and clinical measures of well-being including weight and feeding habits have stabilized. LessonsThese preliminary results suggest xenotransplantation has improved the quality-of-life (QOL) for this animal and holds tremendous therapeutic promise.

neuroscience↗

bioRxiv2020

Attention in Motion: Using an Oddball Task to Record Brain Activity in Skateboarders

Recent advancements in portable computer devices have opened new avenues in the study of human cognition outside research laboratories. This flexibility in methodology has led to the publication of several Electroencephalography (EEG) studies recording brain responses in real-world scenarios such as cycling and walking outside. In the present study, we tested the classic auditory oddball task while participants moved around an indoor running track using an electric skateboard. This novel approach allows for the study of attention in motion while virtually removing body movement. Using the skateboard auditory oddball paradigm, we found reliable and expected standard-target differences in the P3 and MMN/N2b event-related potentials (ERPs). We also recorded baseline EEG activity and found that, compared to this baseline, alpha power is attenuated in frontal and parietal regions during skateboarding. In order to explore the influence of motor interference in cognitive resources during skateboarding, we compared participants preferred riding stance (baseline level of riding difficulty) vs their non-preferred stance (increased level of riding difficulty). We found that an increase in riding difficulty did not modulate the P3 and tonic alpha amplitude during skateboard motion. These results suggest that increases in motor demands might not lead to reductions in cognitive resources as shown in previous literature.

neuroscience↗

bioRxiv2018

Neural engagement with online educational videos predicts learning performance for individual students

Online educational materials are largely disseminated through videos, and yet there is little understanding of how these videos engage students and fuel academic success. We hypothesized that components of the electroencephalogram (EEG), previously shown to reflect video engagement, would be predictive of academic performance in the context of educational videos. Two groups of subjects watched educational videos in either an intentional learning paradigm, in which they were aware of an upcoming test, or in an incidental learning paradigm, in which they were unaware that they would be tested. \"Neural engagement\" was quantified by the inter-subject correlation (ISC) of the EEG that was evoked by the videos. In both groups, students with higher neural engagement retained more information. Neural engagement also discriminated between attentive and inattentive video viewing. These results suggest that this EEG metric is a marker of the stimulus-related attentional mechanisms necessary to retain information. In the future, EEG may be used as a tool to design and assess online educational content.

neuroscience↗