Biology subjects

Marquez-Legorreta, E.

Publications and source records attributed to Marquez-Legorreta, E..

3 recordsLinked to original sources

bioRxiv2025

SpotDMix: informed mRNA transcript assignment using mixture models

Unveiling the genetic profiles of spatially distinguished cells is an important aspect in many areas of brain research, as the genetic identity contains information about a cells physiological properties and internal state. On top of this, knowledge of the genetic details of each cell can reveal structural organization within tissue. As image-based spatial transcriptomics moves toward applications in tissues with dense cellular packing, accurate assignment of detected mRNA transcripts ("spots") to correct segmented cells becomes increasingly difficult, rendering simple methods insufficient with many incorrect assignments to neighboring cells. Here we introduce SpotDMix, a statistical model for assigning spots to cells by modeling spots as coming from a mixture model of distributions matching segmented cell shapes, with assignment probabilities and shape parameters optimized using the Expectation Maximization algorithm. Performance is assessed and compared against several simple methods in various scenarios on both surrogate data and larval zebrafish data. In all tested scenarios SpotDMix outperforms the simple methods on all evaluated metrics, including individual transcript assignment accuracy, total assigned number of spots per cell error and cell type classification. Further, SpotDMix produces a higher degree of exclusivity between genes which are known to not or rarely co-express.

neuroscience↗

bioRxiv2020

Sound generation in zebrafish with Bio-Opto-Acoustics (BOA)

Hearing is a crucial sense in underwater environments for communication, hunting, attracting mates, and detecting predators. However, the tools currently used to study hearing are limited, as they cannot controllably stimulate specific parts of the auditory system. To date, the contributions of hearing organs have been identified through lesion experiments that inactivate an organ, but this makes it difficult to gauge the specific stimuli to which each organ is sensitive, or the ways in which inputs from multiple organs are combined during perception. Here, we introduce Bio-Opto-Acoustic (BOA) stimulation, using optical forces to generate localized sound in vivo, and demonstrate stimulation of the auditory system of zebrafish larvae with unprecedented control. We use a rapidly oscillated optical trap to generate vibrations in individual otolith organs that are perceived as sound, while adjacent otoliths are either left unstimulated or similarly stimulated with a second optical laser trap. The resulting brain-wide neural activity is characterized using fluorescent calcium indicators, thus linking each otolith organ to its individual neuronal network in a way that would be impossible using traditional sound delivery methods. The results reveal integration and cooperation of the utricular and saccular otoliths, which were previously described as having separate biological functions, during hearing.

biophysics↗

bioRxiv2019

Brain-wide visual habituation networks in wild type and fmr1 zebrafish

Habituation is a form of learning during which animals stop responding to repetitive stimuli, and deficits in habituation are characteristics of several psychiatric disorders. Due to the technical challenges of measuring brain activity comprehensively and at cellular resolution, the brain-wide networks mediating habituation are poorly understood. Here we report brain-wide calcium imaging during visual learning in larval zebrafish as they habituate to repeated threatening loom stimuli. We show that different functional categories of loom-sensitive neurons are located in characteristic locations throughout the brain, and that both the functional properties of their networks and the resulting behavior can be modulated by stimulus saliency and timing. Using graph theory, we identify a principally visual circuit that habituates minimally, a moderately habituating midbrain population proposed to mediate the sensorimotor transformation, and downstream circuit elements responsible for higher order representations and the delivery of behavior. Zebrafish larvae carrying a mutation in the fmr1 gene have a systematic shift towards sustained premotor activity in this network, and show slower behavioral habituation. This represents the first description of a visual learning network across the brain at cellular resolution, and provides insights into the circuit-level changes that may occur in people with Fragile X syndrome and related psychiatric conditions.

neuroscience↗