Biology subjects

Alvarez, Y.

Publications and source records attributed to Alvarez, Y..

6 recordsLinked to original sources

bioRxiv2026

NLRP3 activators disrupt the endocytic AP2 complex and plasma membrane signaling

Organellar perturbations are linked to NLRP3 inflammasome activation, however, it remains unclear whether unrelated agonists converge on a common upstream pathway. Here, we traced intracellular organelle and protein movements by differential ultracentrifugation combined with mass spectrometry-based proteomics. We show that NLRP3 activators uniformly disrupt the endocytic Adaptor Protein 2 (AP2) complex, whereas other subcellular rearrangements are stimulus-specific. We discovered Dynasore as a K-efflux-independent NLRP3 activator that engages this signaling node irrespective of endocytosis inhibition. Pharmacological and genetic perturbation of AP2 renders cells unresponsive to extracellular cues, blunting GPCR signaling, cAMP production, and chemotaxis, thereby enforcing a frozen signaling state that propagates NLRP3 inflammasome activation. Collectively, our study reveals a common surveillance checkpoint linking impaired plasma membrane signaling to the execution of inflammation and cell death. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707400v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@178eb1dorg.highwire.dtl.DTLVardef@193cb02org.highwire.dtl.DTLVardef@1f50080org.highwire.dtl.DTLVardef@1f3e3e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Mixture Models Unveil the Origin of the Enigmatic Satyrine Butterfly Genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae).

We provide the first comprehensive analysis of the origin of two enigmatic Satyrinae genera of uncertain affinities. Calisto, the only Satyrinae genus from the West Indies and endemic to these islands, has resisted numerous attempts at phylogenetic placement, regardless of the data type or methods used. Llorenteana, a monotypic genus from northwestern Mexico, has never been included in a molecular phylogenetic study, and past authors have placed it in five different genera and subtribes. We used mostly published genomic data, but also newly sequenced whole genome data from museum specimens and old DNA extracts, extracted BUSCO genes and prepared several datasets. These datasets differed in the degree of heterogeneity and saturation, the number of nucleotide positions used (all positions or only the first two), and were analyzed as nucleotides or as amino acids. We employed several methods for phylogenetic reconstruction using both partitioned and mixture models, as well as ASTRAL, and we inferred divergence times and ancestral areas of origin for Calisto and Llorenteana. The phylogenetic placement of Calisto varied among datasets when we used partitioned models and ASTRAL; however, most datasets resulted in the same relationships under mixture models. Our results suggest that Calisto is part of a clade of Old World origin that colonized the New World from north to south, thus sharing ancestry with Nearctic taxa. Llorenteana constitutes one of the earliest splits within the Euptychiina, a subtribe of Neotropical origin, but descending together with the Pronophilina from Nearctic ancestors. We propose the recognition of Erebiina stat. rev. as the only subtribe comprising the former Calistina syn. nov., Callerebiina syn. nov, Maniolina syn. nov., and Ypthimina syn. nov.

evolutionary biology↗

bioRxiv2024

Gut bacteria-derived succinate induces enteric nervous system regeneration

Enteric neurons control gut physiology by regulating peristalsis, nutrient absorption, and secretion1. Disruptions in microbial communities caused by antibiotics or enteric infections result in the loss of enteric neurons and long-term motility disorders2-5. However, the signals and underlying mechanisms of this microbiota-neuron communication are unknown. We studied the effects of microbiota on the recovery of the enteric nervous system after microbial dysbiosis caused by antibiotics. We found that both enteric neurons and glia are lost after antibiotic exposure, but recover when the pre-treatment microbiota is restored. Using murine gnotobiotic models and fecal metabolomics, we identified neurogenic bacterial species and their derived metabolite succinate as sufficient to rescue enteric neurons and glia. Unbiased single-nuclei RNA-seq analysis uncovered a novel neural precursor-like population marked by the expression of the neuronal gene Nav2. Genetic fate-mapping showed that Plp1+ enteric glia differentiate into neurons following antibiotic exposure. In contrast, Nav2+ neurons expand upon succinate treatment and indicate an alternative mode of neuronal regeneration under recovery conditions. Our findings highlight specific microbial species, metabolites, and the underlying cellular mechanisms involved in neuronal regeneration, with potential therapeutic implications for peripheral neuropathies.

neuroscience↗

bioRxiv2024

Retention of ES cell-derived 129S genome drives NLRP1 hypersensitivity and transcriptional deregulation in Nlrp3-/- mice

Immune response genes are highly polymorphic in humans and mice, with heterogeneity amongst loci driving strain-specific host defense responses. The inadvertent retention of polymorphic loci can introduce confounding phenotypes, leading to erroneous conclusions, and impeding scientific advancement. In this study, we employ a combination of RNAseq and variant calling analyses and identify a substantial region of 129S genome, including the highly polymorphic Nlrp1 locus proximal to Nlrp3, in one of the most commonly used mouse models of NLRP3 deficiency. We show that increased expression of 129S NLRP1b sensitizes Nlrp3-/- macrophages to NLRP1 inflammasome activation. Furthermore, the presence of 129S genome leads to altered gene and protein regulation across multiple cell-types, including of the key tissue-resident macrophage marker, TIM4. To address the challenge of resolving NLRP3-dependent phenotypes, we introduce and validate a conditional Nlrp3 allele, enabling precise temporal and cell-type-specific control over Nlrp3 deletion. Our study establishes a generic framework to identify functionally relevant SNPs and assess genomic contamination in transgenic mice. This allows for unambiguous attribution of phenotypes to the target gene and advances the precision and reliability of research in the field of host defense responses.

immunology↗

bioRxiv2021

Affordable and Effective Optokinetic Response Methods to Assess Visual Acuity and Contrast Sensitivity in Larval to Juvenile Zebrafish

BackgroundThe optokinetic response (OKR) is an effective behavioural assay to investigate functional vision in zebrafish. The rapid and widespread use of gene editing, drug screening and environmental modulation technologies have resulted in a broader need for visual neuroscience researchers to access affordable and more sensitive OKR, contrast sensitivity (CS) and visual acuity (VA) assays. Here, we demonstrate how 2D- and 3D-printed, striped patterns or drums coupled with a motorised base and microscope provide a simple, cost-effective but efficient means to assay OKR, CS and VA in larval-juvenile zebrafish. ResultsIn wild-type, 5 days post-fertilisation (dpf) zebrafish, the 2D or 3D drums printed with the standard OKR stimulus of 0.02 cycles per degree (cpd), 100% black-white contrast evoked equivalent responses of 24.2 or 21.8 saccades per minute, respectively. Furthermore, although the OKR number was significantly reduced compared to the 0.02 cpd drum (p<0.0001), the 2D and 3D drums evoked respectively equivalent responses with the 0.06 and 0.2 cpd drums. Notably, standard OKR responses varied with time of day; peak responses of 29.8 saccades per minute occurred in the early afternoon with significantly reduced responses occurring in the early morning or late afternoon, (18.5 and 18.4 saccades per minute, respectively). A customised series of 2D printed drums enabled analysis of visual acuity and contrast sensitivity in 5-21 dpf zebrafish. The saccadic frequency in visual acuity and contrast sensitivity assays, was inversely proportional to age, spatial frequency and contrast of the stimulus. ConclusionsOKR, VA and CS of zebrafish larvae can be efficiently measured using 2D- or 3D-printed striped drums. For data consistency the luminance of the OKR light source, the time of day when the analysis performed, and the order of presentation of VA and CS drums must be considered. These simple methods allow effective and more sensitive analysis of functional vision in zebrafish.

neuroscience↗

bioRxiv2019

Orthogonal Drug Pooling Enhances Phenotype-based Discovery of Ocular Anti-angiogenic Drugs in Zebrafish Larvae

Unbiased screening of large randomized chemical libraries in vivo is a powerful tool to find new drugs and targets. However, forward chemical screens in zebrafish can be time consuming and usually >99% of test compounds have no significant effect on the desired phenotype. Here, we sought to find bioactive drugs more efficiently and to comply with the 3R principles of replacement, reduction and refinement of animals in research. We investigated if pooling of drugs to simultaneously test 8-10 compounds in zebrafish larvae can increase the screening efficiency of an established assay that identifies drugs inhibiting developmental angiogenesis in the eye. In a phenotype-based screen, we tested 1760 small molecule compounds from the ChemBridge DIVERSet chemical library for their ability to inhibit the formation of distinct primary hyaloid vessels in the eye. Applying orthogonal pooling of the chemical library, we treated zebrafish embryos from 3 to 5 days post fertilization with pools of 8 or 10 compounds at 10 M each. This reduced the number of tests from 1760 to 396. In 63% of cases, treatment showed sub-threshold effects of <40% reduction of primary hyaloid vessels. From 18 pool hits, we identified 8 compounds that reduce hyaloid vessels in the larval zebrafish eye by at least 40%. Compound 4-[4-(1H-benzimidazol-2-yl)phenoxy]aniline ranked as the most promising candidate with reproducible and dose-dependent effects. To our knowledge, this is the first report of a self-deconvoluting matrix strategy applied to drug screening in zebrafish. We conclude that the orthogonal drug pooling strategy is a cost-effective, time-saving and unbiased approach to discover novel inhibitors of developmental angiogenesis in the eye. Ultimately, this approach may identify new drugs or targets to mitigate disease caused by pathological angiogenesis in the eye e.g. diabetic retinopathy or age-related macular degeneration wherein blood vessel growth and leaky vessels lead to vision impairment or clinical blindness.

pharmacology and toxicology↗