Biology subjects

Ripoll, J.

Publications and source records attributed to Ripoll, J..

4 recordsLinked to original sources

bioRxiv2025

White and Clearing: New Optical Tissue Clearing Method

AbstractOptical tissue clearing techniques can render large-scale tissue samples and whole organs transparent to apply cell-resolution 3D imaging techniques, revolutionizing the fields of biological research and pathological diagnosis, and providing never-before seen structural information. There are several widely used protocols, but they have shortcomings, both in complexity of use and in suboptimal results in certain tissues and organs. Here, we describe a new method dubbed "White and Clear" (WaC) using 2,2-thiodiethanol (TDE) as a dynamic Refractive Index (RI)-matching reagent alongside a lipid-extraction and a pigment-bleaching step using dilute hydrogen peroxide (H2O2), to provide ease of use and enhanced clearing effect on all kinds of samples and allow for the clearing parameters to be finely adjusted in order to obtain the best results in each situation.

physiology↗

bioRxiv2022

dipwmsearch: a python package for searching di-PWM motifs

MotivationSeeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites (TFBS). Useful motif representations include Position Weight Matrices (PWMs), dinucleotidic PWMs (di-PWMs), and Hidden Markov Models (HMMs). Dinucleotidic PWMs combine the simplicity of PWMs - a matrix form and a cumulative scoring function -, but also incoporate dependency between adjacent positions in the motif (unlike PWMs which disregard any dependency). For instance, to represent binding sites, the HOCOMOCO database provides di-PWM motifs derived from experimental data. Currently, two programs, SPRy-SARUS and MOODS, can search for di-PWMs in sequences. ResultsWe propose a Python package, dipwmsearch, which provides an original and efficient algorithm for this task (it first enumerates matching words for the di-PWM, and then search them at once in the sequence even if it contains IUPAC codes). The user benefits from an easy installation via Pypi or conda, a documented Python interface, and reusable example scripts that smooth the use of di-PWMs. Availability and Implementationdipwmsearch is available at https://pypi.org/project/dipwmsearch/ and https://gite.lirmm.fr/rivals/dipwmsearch/ under Cecill license.

bioinformatics↗

bioRxiv2021

Non-invasive visualization of amyloid-beta deposits in Alzheimer amyloidosis mice using magnetic resonance imaging and fluorescence molecular tomography

Abnormal cerebral accumulation of amyloid-beta peptide (A{beta}) is a major hallmark of Alzheimers disease. Non-invasive monitoring of A{beta} deposits enables assessing the disease burden in patients and animal models mimicking aspects of the human disease as well as evaluating the efficacy of A{beta}-modulating therapies. Previous in vivo assessments of plaque load in mouse models of cerebral amyloidosis have been predominantly based on two-dimensional diffuse fluorescence reflectance imaging (2D-FRI) and two-photon microscopy (2PM) using A{beta}-specific imaging agents. However, 2D-FRI lacks depth resolution, whereas 2PM is restricted by the limited field of view preventing coverage of large brain regions. Here, we utilized a magnetic resonance imaging (MRI) and fluorescence molecular tomography (FMT) pipeline with the curcumin derivative fluorescent probe CRANAD-2 to achieve full 3D brain coverage for detecting A{beta} accumulation in the arcA{beta} mouse model of cerebral amyloidosis. A homebuilt FMT system was used for data acquisition in combination with a customized software platform enabling the integration of anatomical information derived from MRI as prior information for FMT image reconstruction. The results obtained from the FMT-MRI study were compared to data obtained from conventional 2D-FRI recorded under similar physiological conditions. The two methods yielded comparable time courses of the fluorescence intensity following intravenous injection of CRANAD-2 in a region of interest comprising the mouse brain. The depth resolution inherent to FMT allowed separation of signal contributions from the scalp and different brain regions, indicating preferential accumulation of the fluorescent tracer in the cerebral cortex, a region characterized by significant plaque deposition in arc A{beta} mice. In conclusion, we have demonstrated the feasibility of visualizing A{beta} deposition in 3D using a multimodal FMT-MRI method. This hybrid imaging method provides complementary anatomical, physiological and molecular information, thereby enabling the detailed characterization of the disease status in mouse models of cerebral amyloidosis, which is also important for monitoring the efficacy of putative treatments targeting A{beta}.

neuroscience↗

bioRxiv2018

Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling

Genetic alterations in human BCL9 genes have repeatedly been found in congenital heart disease (CHD) with as-of-yet unclear causality. BCL9 proteins and their Pygopus (Pygo) co-factors can participate in canonical Wnt signaling via binding to {beta}-catenin. Nonetheless, their contributions to vertebrate heart development remain uncharted. Here, combining zebrafish and mouse genetics, we document tissue-specific functions in canonical Wnt signaling for BCL9 and Pygo proteins during heart development. In a CRISPR-Cas9-based genotype-phenotype association screen, we uncovered that zebrafish mutants for bcl9 and pygo genes largely retain {beta}-catenin activity, yet develop cardiac malformations. In mouse, both systemic and lineage-specific loss of the Pygo-BCL9-{beta}-catenin complex caused heart defects with outflow tract malformations, aberrant cardiac septation and valve formation, and compact myocardium hypoplasia. Mechanistically, these phenotypes coincide with transcriptional deregulation during heart patterning, and Pygo2 associates with {beta}-catenin at cis-regulatory regions of cardiac genes. Taken together, our results establish BCL9 and Pygo as tissue-specific {beta}-catenin co-factors during vertebrate heart development. Our results further implicate alterations in BCL9 and BCL9L in human CHDs as possibly causative.

genetics↗