Biology subjects

Ribeiro, B.

Publications and source records attributed to Ribeiro, B..

8 recordsLinked to original sources

bioRxiv2026

ZonationR: An R interface to the Zonation software for reproducible spatial conservation prioritisation workflows

Systematic conservation planning provides a science-based framework for defining conservation goals and supporting transparent spatial decision-making under limited resources. Within this framework, spatial conservation prioritisation tools are widely used to identify areas of high biodiversity value by integrating information on species distributions, connectivity, costs, and other factors into spatially explicit recommendations. Zonation is one of the leading software tools in this field, producing hierarchical priority rankings of landscapes based on conservation value. However, its standard workflow typically relies on manual steps for data preparation, execution, and post-processing, which can become inefficient and difficult to reproduce when multiple scenarios are analysed, limiting accessibility and broader uptake. We introduce ZonationR, an R package that provides a streamlined interface to the Zonation software, enabling fully reproducible and automated spatial prioritisation workflows. The package integrates the entire analysis pipeline, encompassing input preparation, execution of Zonation, and post-processing, while supporting both single-variant and multi-variant workflows. ZonationR also provides tools to explore and interpret outputs, including priority maps, feature performance curves, cost summaries, feature representation metrics, and similarity assessments between prioritisation solutions. By linking directly to the original Zonation engine, the package enables users to benefit from ongoing methodological developments in Zonation and access its functionality through a transparent, script-based workflow, thereby reducing technical barriers to running and understanding spatial prioritisation analyses. Beyond these advantages, its integration within the R environment supports iterative testing of conservation scenarios and more rigorous assessment of methodological decisions, while facilitating seamless connections with wider ecological workflows (e.g., species distribution modelling). As conservation planning increasingly relies on large, complex, multi-source datasets and integrative approaches, such integration is essential for enabling robust, transparent, and reproducible decision-making across spatial scales.

bioinformatics↗

bioRxiv2025

Late INa activation of cardiac TTX-sensitive sodium channels by AaH-II induces an arrhythmogenic phenotype

AimsLate sodium current (INaL) is a key contributor to cardiac arrhythmias, but its precise origin and arrhythmogenic potential from tetrodotoxin-sensitive (TTX-S) sodium (Nav) channels remain unclear. While the FDA-endorsed toxin ATX-II has been widely used to model INaL-associated arrhythmogenesis, it lacks selectivity, limiting its utility in dissecting the roles of individual Nav channel subtypes. This study investigates the proarrhythmic impact of TTX-S Nav channel activation using AaH-II*, a scorpion venom-derived peptide with selective efficacy for TTX-S channels. Methods and ResultsUsing automated patch-clamp recordings, we characterized AaH-II* selectivity across human Nav isoforms and demonstrated potent, preferential activation of INaL in hNav1.1, 1.2, 1.3, and 1.6 over the TTX-resistant cardiac isoform hNav1.5. Calcium imaging in isolated adult rat cardiomyocytes showed that low nanomolar concentrations of AaH-II* induced spontaneous calcium release events and arrhythmogenic calcium transients, even in the absence of Nav1.5 activation. Ex vivo multielectrode array recordings in Langendorff-perfused rat hearts confirmed dose-dependent ventricular conduction slowing, prolonged repolarization, and increased arrhythmia burden, all mitigated by TTX. In vivo, intravenous AaH-II* administration in rats elicited QTc prolongation, atrioventricular block, and ventricular tachyarrhythmias, which were significantly suppressed by TTX pretreatment. ConclusionWe identify AaH-II* as a powerful and selective tool to study INaL from TTX-S Nav channels in cardiac tissue. Our findings reveal that TTX-S channel-mediated INaL alone is sufficient to induce arrhythmias and that pharmacological inhibition of these channels offers a promising antiarrhythmic strategy. These results advocate for broader consideration of TTX-S Nav channels as targets in arrhythmia research and drug safety screening.

physiology↗

bioRxiv2025

Electrophysiological classification of CACNA1G gene variants associated with neurodevelopmental and neurological disorders

This study highlights the complementarity of automated patch-clamp (APC) and manual patch-clamp (MPC) approaches to describe the electrophysiological properties of eighteen Cav3.1 calcium channel variants associated with various neurological conditions. Current density was measured efficiently for all variants in APC experiments, with four variants (p.V184G, p.N1200S, p.S1263A and p.D2242N) showing high current densities, compared to wild-type Cav3.1 channel, while six variants (p.M197R, p.V392M, p.F956del, p.I962N, p.I1412T, and p.G1534D) displayed low current densities, and were therefore preferentially studied using MPC. The electrophysiological properties were well conserved in APC (e.g. inactivation and deactivation kinetics, steady-state properties), with only the APC-MPC correlation for the activation kinetics being less robust. In addition, neuronal modeling, using a deep cerebellar neuron (DCN) environment, revealed that most of the variants localized in the intracellular gate (S5 and S6 segments) could increase DCN spike frequencies. This DCN firing was critically dependent on the current density and further pointed to the gain-of-function (GOF) properties of p.A961T and p.M1531V, the recurrent variants associated with Spinocerebellar Ataxia type-42 with Neurodevelopmental Deficit (SCA42ND). Action-potential (AP) clamp experiments performed using cerebellar and thalamic neuron activities further established the GOF properties of p.A961T and p.M1531V variants. Overall, this study demonstrates that APC is well-suited to high-throughput analysis of Cav3.1 channel variants, and that MPC complements APC for characterizing low-expression variants. Furthermore, in silico modeling and AP clamp experiments establish that the gain- or loss-of-function properties of the variants are determined by how the Cav3.1 channel decodes the electrophysiological context of a neuron.

neuroscience↗

bioRxiv2023

BeeDC: An R package and globally synthesised and flagged bee occurrence dataset

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.

ecology↗

bioRxiv2023

Predicting hERG repolarization power at 37°C from recordings at room temperature

Mutations in the KCNH2 gene cause long or short QT syndromes (LQTS or SQTS) predisposing to life-threatening arrhythmias. KCNH2 encodes for the voltage-gated K+ channel hERG involved in the late repolarization phase of the cardiac action potential (AP). For the last decades, sequencing KCNH2 has provided a plethora of variants associated or not with clear pathological cardiac phenotypes. Identifying pathogenic or likely pathogenic variants from the benign ones would provide useful information to clarify the genetic background of LQTS patients and relatives, and to stratify the risk of adverse events. In face of a wide spectrum of hERG biophysical defects, we looked for a way to summarize the net loss or gain of function in a unique index. In a previous work, we defined as the repolarization power the time integral of the K+ currents developed during an AP clamp. Here, with the aim of accelerating the functional characterization of hERG variants using automated patch-clamp, we adapted the AP-clamp protocol to establish, at room temperature, at which the recording success rate is high, a repolarization power index, as reliable and informative as the one measured at physiological temperature. We also illustrate that the repolarization power determined at room temperature is predictive of the repolarization power at physiological temperature for 2 pathogenic hERG variants with different biophysical dysfunctions.

physiology↗

bioRxiv2023

Optical control of cardiac rhythm by in vivo photoactivation of an ERG channel peptide inhibitor

RATIONALECardiac rhythm, conduction and synchronization of electrical activity require the coordinated action of different types of ion channels that differ according to transmural and regional specificities. Classical pharmacology affects these ion channels in a non-regionalized way which explains why treating arrhythmias, that often occur in specific foci, has often limited efficacy in addition to negative side-effects on non-targeted organs. Photopharmacology is an emergent technology that has the potential to counteract all the negative aspects of classical pharmacology by restricting drug activity in a spatio-temporal manner. OBJECTIVEWe tested the potential of photopharmacology in specifically regulating heart activity by using a caged derivative of a natural peptide inhibitor of the ERG channel, BeKm1. The peptide was uncaged and activity monitored in vitro on a cell line expressing the hERG channel, on human cardiomyocytes derived from iPS cells, and ex vivo and in vivo on zebrafish larvae and rat hearts. METHODS AND RESULTSCaged BeKm-1 is inactive and fully active upon uncaging. Uncaging of the peptide on human iPS-derived cardiomyocytes enlarges the action potential duration and triggers arrhythmias. Uncaging also triggers bradycardia and disturbs cardiac conduction within the atria in perfused rat hearts upon illumination. The potency of photopharmacology for cardiac electrical modulation was further validated in zebrafish larvae where illumination of the caged compound induces bradycardia and atrio-ventricular desynchrony. Finally, in anesthetized rats, illumination of the caged peptide in the right atria, containing the sino-atrial node, leads to bradycardia without arrhythmia. CONCLUSIONSThis report demonstrates that photopharmacology, using the caged peptide strategy, can be used for dynamically regulating cardiac electrical activity in vivo and that spatial illumination restriction can dissociate the bradycardic effect from the arrhythmic one. The technology is applicable to all kinds of cardiac ion channels and regions of interest to create arrhythmogenic models or investigate new clinical applications.

pharmacology and toxicology↗

bioRxiv2020

ER-Anchored Transcription Factors bZIP17 and bZIP60 Regulate Triterpene Saponin Biosynthesis in Medicago truncatula

Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA-modulated basic helix-loop-helix (bHLH) transcription factors (TFs), TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR 1 (TSAR1) and TSAR2, have been previously identified as direct activators of TS biosynthesis in the model legume Medicago truncatula. Here, we report on the involvement of the core endoplasmic reticulum (ER) stress basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing of M. truncatula bZIP17 and bZIP60 proteins was altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure. M. truncatula bZIP17 and bZIP60 proteins were shown to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes, particularly under ER stress conditions, when they translocate from the ER to the nucleus. Furthermore, the inhibitory role of ER stress bZIP TFs in the regulation of JA-dependent terpene biosynthetic pathways appears to be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus. We postulate that activation of ER stress bZIP TFs provides the plant with a mechanism to balance metabolic activities and thereby adequately govern modulation of growth, development and defense processes in defined stress situations. One sentence summaryER stress bZIP transcription factors can interfere with the activity of jasmonate-inducible bHLH transcription factors to modulate the elicitation of plant specialized metabolism in stress conditions.

plant biology↗

bioRxiv2018

High-throughput yeast two-hybrid library screening using next generation sequencing

Yeast two-hybrid (Y2H) is a well-established genetics-based system that uses yeast to selectively display binary protein-protein interactions (PPIs). To meet the current need to unravel complex PPI networks, several adaptations have been made to establish medium- to high-throughput Y2H screening platforms, with several having successfully incorporated the use of the next-generation sequencing (NGS) technology to increase the scale and sensitivity of the method. However, these have been to date mainly restricted to the use of fully annotated custom-made open reading frame (ORF) libraries and subject to complex downstream data processing. Here, a streamlined high-throughput Y2H library screening strategy, based on integration of Y2H with NGS, called Y2H-seq, was developed, which allows efficient and reliable screening of Y2H cDNA libraries. To generate proof of concept, the method was applied to screen for interaction partners of two key components of the jasmonate signaling machinery in the model plant Arabidopsis thaliana, resulting in the identification of several previously reported as well as hitherto unknown interactors. Our Y2H-seq method offers a user-friendly, specific and sensitive screening method that allows high-throughput identification of PPIs without prior knowledge of the organisms ORFs, thereby extending the method to organisms of which the genome has not entirely been annotated yet. The quantitative NGS readout and the incorporation of background controls allow to increase genome coverage and ultimately dispose of recurrent false positives, thereby overcoming some of the bottlenecks of current Y2H technologies, which will further strengthen the value of the Y2H technology as a discovery platform.

molecular biology↗