Biology subjects

Barrios, A.

Publications and source records attributed to Barrios, A..

11 recordsLinked to original sources

bioRxiv2026

Distinct thresholds condition sense PTGS initiation and amplification.

It has long been known that Pro35S-driven sense transgenes have a high propensity to undergo post-transcriptional gene silencing (S-PTGS). However, what exactly conditions S-PTGS initiation and amplification to make it systemic remains unknown. Through genetic screens, we show that antagonistic chromatin-related mutations enhancing and reducing transgene expression, result in enhanced and reduced S-PTGS amplification capacities, respectively, without affecting the initiation rate. Analysis of a large set of independent transgenic plants confirm a direct relationship between transgene expression and its capacity to amplify S-PTGS. Combining an inducible or a tissue-specifically expressed GUS transgene with a Pro35S:GUS transgene locus prone to amplify S-PTGS but unable to spontaneously initiate it induces systemic S-PTGS, indicating that transient and/or local passing of a discrete threshold is sufficient to initiate S-PTGS. Together, these results call for the existence of distinct thresholds related to transiently produced aberrant RNA and permanently produced target mRNA levels, which condition S-PTGS initiation and amplification, respectively. We show that this model also applies to endogenous genes for which RNA Quality Control (RQC) acts as a first layer of protection against S-PTGS, and DCL2s obscuration by DCL4 as a second layer, allowing RQC to dysfunction locally without translating into the drama of systemic S-PTGS.

plant biology↗

bioRxiv2026

The Euler Characteristic Transform Enables Classification of Complex Plant Shapes and Prediction of Leaf Venation from Blade Geometry

(1) RationaleQuantifying and predicting plant morphology is central to understanding development and evolution, yet many plant forms lack homologous features required for traditional morphometrics. We apply the Euler Characteristic Transform (ECT), an injective descriptor from topological data analysis, to encode 2D plant shapes. The ECT converts contours into image-like representations that preserve shape information while enabling deep learning. (2) MethodsWe computed ECTs for large datasets of leaf and pavement cell shapes and used convolutional neural networks (CNNs) for classification. We also trained CNNs to approximate the inverse mapping, predicting leaf shape masks from radial ECTs. (3) Key resultsECT-based models achieved high classification accuracy, surpassing previous approaches on millions of herbarium-derived leaves. Notably, grapevine leaf venation was predicted from blade geometry alone, demonstrating that vascular structure is encoded in the outline. (4) Main conclusionThe ECT provides a compact, information-preserving representation of biological shape that integrates naturally with deep learning. It enables both accurate classification and predictive reconstruction, revealing latent morphological information and offering new opportunities to study plant form across scales.

plant biology↗

bioRxiv2025

mRNA and Protein Expression of Fetal Insulin Receptor in Breast Cancer Cell Lines

The insulin receptor (IR) is expressed in breast cancer cells and plays a role in regulating tumor biology. There are two IR isoforms generated from the same gene. Alternate splicing with exclusion or inclusion of exon 11accounts for the two isoforms. The exon 11 excluded isoform (IR-A) is expressed during fetal development while the full-length adult IR (IR-B) is the primary form expressed during adult life. This splice variant results in a 12 amino acid variation in peptide sequence. Breast cancer cells overexpress IR-A with an increased IR-A:IR-B ratio. Most of these data were obtained by examining mRNA expressions. In this work, we examined over 40 breast cancer cell lines and patient tumor samples for mRNA expression of the IR isoforms to show that most cells overexpressed IR-A compared to IR-B. Further we used mass spectrometry to demonstrate IR-A protein expression in the Du4475 cell line which has a high level of IR-A mRNA expression. To our knowledge, this is the first demonstration of IR-A protein expression. Thus, IR-A mRNA and protein expression demonstrate a potential role for this insulin receptor isoform in breast cancer biology.

cancer biology↗

bioRxiv2025

Pervasive homeobox gene function in the male-specific nervous system of Caenorhabditis elegans

We explore here how neuronal cell type diversity is genetically delineated in the context of the large, but poorly studied male-specific nervous system of the nematode Caenorhabditis elegans. Mostly during postembryonic development, the C. elegans male adds 93 male-specific neurons, falling into 25 cardinal classes, to the predominantly embryonically generated, sex-shared nervous system, comprised of 294 neurons (116 cardinal classes). Using engineered reporter alleles, we investigate here the expression pattern of 40 phylogenetically conserved homeodomain proteins within the male-specific nervous system of C. elegans, demonstrating that in aggregate, the expression of these homeodomain proteins covers each individual male-specific neuron. We show that the male-specific nervous system can be subdivided along the anterior/posterior axis in HOX cluster expression domains. The extent of our expression analysis predicts that each individual neuron class is likely defined by unique combinations of homeodomain proteins. Using a collection of newly available molecular markers, we undertake a mutant analysis of five of these genes (unc-30, unc-42, lim-6, lin-11, ttx-1) and identified defects in cell fate specification and/or male copulatory defects in each of these mutant strains. Our analysis expands our understanding of the importance of homeobox genes in nervous system development and function.

neuroscience↗

bioRxiv2025

Gene regulatory mechanisms underlying evolutionary adaptations of homologous neuronal cell types

How nervous systems coordinate the generation of specific neuron types with gene expression plasticity and how these mechanisms impact cell type evolution is unknown. Here we use Caenorhabditis species to study neuron-type robustness, plasticity and evolution, using VC4 and VC5 cholinergic motoneurons as models. In C. elegans, we found that epigenetic silencing through histone 3 lysine 9 methylation (H3K9me) is necessary to suppress the expression of the serotonin reuptake gene mod-5/Sert and a serotonergic phenotype in these cells. In contrast, we observed that VC4 and VC5 neurons in the Angaria group of species of the Caenorhabditis genus have evolved an intense serotonergic staining. This phenotype is caused by the emergence of a new enhancer in the mod-5/Sert locus, which has been recruited to the ancestral neuron-type gene regulatory network. Enhancer transfer from C. angaria is sufficient to impose a constitutive serotonergic fate in C. elegans. Remarkably, acquiring this new trait modulates egg-laying responses to high levels of exogenous serotonin, which can be found in specific environments. Finally, we discovered that the repression of the serotonergic fate in C. elegans VC4 and VC5 neurons is indeed a plastic trait that can be adjusted in specific environmental growth conditions to elicit egg-laying behaviours similar to those observed in Angaria species. Our work identifies gene regulatory mechanisms that coordinate the generation of robust neuron-type-specific programs with plastic gene expression responses. These findings identify a gene regulatory framework underlying the evolution of neuron-type-specific features and the emergence of novel behaviours.

evolutionary biology↗

bioRxiv2023

The transcription factor NF-YA10 determines the area explored by Arabidopsis thaliana roots through direct regulation of LAZY and TAC genes

Root developmental plasticity relies on transcriptional reprogramming, which largely depends on the activity of transcription factors (TFs). NF-YA2 and NF-YA10 (Nuclear Factor A2 and A10) are down-regulated by the specific miRNA isoform miR169defg, in contrast to miR169a. Here, we analyzed the role of the Arabidopsis thaliana TF NF-YA10 in the regulation of lateral root development. Plants expressing a version of NF-YA10 resistant to miR169 cleavage showed a perturbation in the lateral root gravitropic response. By extracting novel features of root architecture using the ChronoRoot deep-learning-based phenotyping system, we uncovered a differential emergence angle of lateral roots over time when compared to Col-0. Detailed phenotyping of root growth dynamics revealed that NF-YA10 activity modulates the area explored by Arabidopsis roots. Furthermore, we found that NF-YA10 directly regulates TAC1 and LAZY genes by targeting their promoter regions, genes previously linked to gravitropism. Hence, the TF NF-YA10 is a new element in the control of LR gravitropism and root system architecture.

plant biology↗

bioRxiv2023

C. elegans males optimize mate-choice decisions via sex-specific responses to multimodal sensory cues

For sexually reproducing animals, selecting optimal mates is essential for maximizing reproductive fitness. Because the nematode C. elegans reproduces mostly by self-fertilization, little is known about its mate-choice behaviors. While several sensory cues have been implicated in males ability to recognize hermaphrodites, achieving an integrated understanding of the ways males use these cues to assess relevant characteristics of potential mates has proven challenging. Here, we use a choice-based social-interaction assay to explore the ability of C. elegans males to make and optimize mate choices. We find that males use a combination of volatile sex pheromones (VSPs), ascaroside pheromones, surface-bound chemical cues, and other signals to robustly assess a variety of features of potential mates. Specific aspects of mate choice are communicated by distinct signals: the presence of a sperm-depleted, receptive hermaphrodite is likely signaled by VSPs, while developmental stage and sex are redundantly specified by ascaroside pheromones and surface-associated cues. Ascarosides also signal nutritional information, allowing males to choose well-fed over starved mates, while both ascarosides and surface-associated cues cause males to prefer virgin over previously mated hermaphrodites. The male-specificity of these behavioral responses is determined by both male-specific neurons and the male state of sex-shared circuits, and we reveal an unexpected role for the sex-shared ASH sensory neurons in male attraction to endogenously produced hermaphrodite ascarosides. Together, our findings lead to an integrated view of the signaling and behavioral mechanisms by which males use diverse sensory cues to assess multiple features of potential mates and optimize mate choice.

neuroscience↗

bioRxiv2023

Conflict during learning reconfigures the neural representation of positive valence and approach behaviour

Punishing and rewarding experiences can change the valence of sensory stimuli and guide animal behaviour in opposite directions, resulting in avoidance or approach. Often, however, a stimulus is encountered with both positive and negative experiences. How is such conflicting information represented in the brain and resolved into a behavioural decision? We address this question by dissecting a circuit for sexual conditioning in C. elegans. In this learning paradigm, an odour is conditioned with both a punishment (starvation) and a reward (mates) resulting in odour approach. We find that negative and positive experiences are both encoded by the neuropeptide PDF-1 being released from and acting on different neurons. Each experience creates a separate, parallel memory in the circuit for odour processing. This results in the sensorimotor representation of odour being different in naive and sexually conditioned animals despite both displaying approach. Our results reveal that the positive valence of a stimulus is not represented in the activity of any single neuron class but flexibly represented within the circuit according to the experiences and predictions associated with the stimulus.

neuroscience↗

bioRxiv2022

COVID-19 Causes Ciliary Dysfunction as Demonstrated by Human Intranasal Micro-Optical Coherence Tomography Imaging

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), causative agent of coronavirus disease 2019 (COVID-19), binds via ACE2 receptors, highly expressed in ciliated cells of the nasal epithelium. Micro-optical coherence tomography (OCT) is a minimally invasive intranasal imaging technique that can determine cellular and functional dynamics of respiratory epithelia at 1-m resolution, enabling real time visualization and quantification of epithelial anatomy, ciliary motion, and mucus transport. We hypothesized that respiratory epithelial cell dysfunction in COVID-19 will manifest as reduced ciliated cell function and mucociliary abnormalities, features readily visualized by OCT. Symptomatic outpatients with SARS-CoV-2 aged [≥] 18 years were recruited within 14 days of symptom onset. Data was interpreted for subjects with COVID-19 (n=13) in comparison to healthy controls (n=8). Significant reduction in functional cilia, diminished ciliary beat frequency, and abnormal ciliary activity were evident. Other abnormalities included denuded epithelium, presence of mucus rafts, and increased inflammatory cells. Our results indicate that subjects with mild but symptomatic COVID-19 exhibit functional abnormalities of the respiratory mucosa underscoring the importance of mucociliary health in viral illness and disease transmission. Ciliary imaging enables investigation of early pathogenic mechanisms of COVID-19 and may be useful for evaluating disease progression and therapeutic response. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/499336v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1f4bb17org.highwire.dtl.DTLVardef@271438org.highwire.dtl.DTLVardef@1a08762org.highwire.dtl.DTLVardef@184847_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Introduction of loxP sites by electroporation in the mouse genome; a simple approach for conditional allele generation in complex targeting loci.

BackgroundThe discovery of the CRISPR-Cas9 system and its applicability in mammalian embryos has revolutionized the way we generate genetically engineered animal models. To date, models harbouring conditional alleles (i.e.: two loxP sites flanking an exon or a critical DNA sequence of interest) remain the most challenging to generate as they require simultaneous cleavage of the genome using two guides in order to properly integrate the repair template. In the current manuscript, we describe a modification of the sequential electroporation procedure described by Horii et al (2017). We demonstrate production of conditional allele mouse models for eight different genes via one of two alternative strategies: either by consecutive sequential electroporation (strategy A) or non-consecutive sequential electroporation (strategy B). ResultsBy using strategy A, we demonstrated successful generation of conditional allele models for three different genes (Icam1, Lox, and Sar1b), with targeting efficiencies varying between 5 to 13%. By using strategy B, we generated five conditional allele models (Loxl1, Pard6a, Pard6g, Clcf1, and Mapkapk5), with targeting efficiencies varying between 3 to 25%. ConclusionOur modified electroporation-based approach, involving one of the two alternative strategies, allowed the production of conditional allele models for eight different genes via two different possible paths. This reproducible method will serve as another reliable approach in addition to other well-established methodologies in the literature for conditional allele mouse model generation.

molecular biology↗

bioRxiv2018

A direct glia-to-neuron natural transdifferentiation ensures nimble sensory-motor coordination of male mating behaviour

The coordinated execution of innate, stereotyped sexual behaviours, such as courtship and mating, requires sexually dimorphic sensory-motor circuits that are genetically specified during development (reviewed in [1-3]). Studies in the nematode Caenorhabditis elegans, in which the development and function of neural circuits can be interrogated with single cell resolution, have revealed two general developmental mechanisms underlying sexual dimorphism in the nervous system. The first involves the acquisition of sexually dimorphic features in sex-shared neurons during sexual maturation, which include changes in terminal gene expression, such as odorant receptors, neurotransmitters and synaptic regulators [4-10]. The second mechanism involves the generation of sex-specific neurons [11-13]. This requires sex-specific cell death [14]or neurogenesis events resulting from extensive sex differences in the cell division patterns and neurodevelopmental programmes of post-embryonic cell lineages (reviewed in [3]). Here we identify a third, novel way to generate sexual dimorphism in the nervous system. We find that during sexual maturation (L4 stage), a class of sex-shared glial cells acquires sexually dimorphic function by undergoing a direct glia-to-neuron transdifferentiation that results in the production of male-specific neurons. This plasticity is regulated cell-intrinsically by the sex-determination pathway. These previously unnoticed neurons, which we term PHDs, are putative proprioceptors that regulate male locomotion during specific steps of mating. One of these steps is a novel readjustment movement performed when intromission becomes difficult to achieve. Our results reveal sex-specific direct transdifferentiation as a novel mechanism for generating sex-specific neurons and also show the importance of proprioceptive feedback during the complex steps of mating for successful reproduction.

neuroscience↗