Biology subjects

Tapia, J. C.

Publications and source records attributed to Tapia, J. C..

3 recordsLinked to original sources

bioRxiv2025

Mitochondrial genome rearrangements and virulence-associated features in a clinical isolate of the emerging pathogen Wickerhamomyces anomalus

BackgroundWickerhamomyces anomalus, also known as Candida pelliculosa, traditionally regarded as an environmental yeast, has emerged as an opportunistic yeast implicated in invasive infections and hospital outbreaks, especially among neonatal and immunocompromised individuals. Despite its clinical relevance, the genomic determinants underlying the pathogenesis and virulence remain poorly understood. ResultsHere, we report the first high-quality nuclear and complete mitochondrial genome assemblies from a clinical isolate of W. anomalus. The nuclear genome spans 13.9 Mb with 34.5% GC content and contains 6,305 protein-coding genes, 8,235 coding sequences, and 147 tRNAs, with 98.1% completeness by BUSCO. The mitochondrial genome (47.6 kb) encodes 19 protein-coding genes, 26 tRNAs, and two rRNAs. Remarkably, it exhibits atypical rearrangements, including inverted repeats and atp9 duplications. ConclusionsWe provide the first de novo nuclear genome from a clinical W. anomalus isolate, along with the first complete mitochondrial genome for this species, establishing a high-quality reference for this emerging pathogen. The genomic innovations, together with a high content of repetitive and non-coding elements, suggest enhanced plasticity that may underpin metabolic flexibility and survival under host-associated stresses. These rearrangements represent an underappreciated mechanism of adaptation in emerging fungal pathogens, contributing to the clinical relevance of W. anomalus. These genomic resources facilitate rigorous comparative analyses to indentify determinants of pathogenicity, virulence, and antifungal resistance, accelerating the development of improved diagnostics, surveillance, and management strategies for W. anomalus infections

genetics↗

bioRxiv2025

A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain

We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing >180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain.

neuroscience↗

bioRxiv2017

Correlated Light-Serial Scanning Electron Microscopy (CoLSSEM) for ultrastructural visualization of single neurons in vivo

A challenging aspect of neuroscience revolves around mapping the synaptic connections within neural circuits (connectomics) over scales spanning several orders of magnitude (nanometers to meters). Despite significant improvements in serial section electron microscopy (SSEM) technologies, several major roadblocks have impaired its general applicability to mammalian neural circuits. In the present study, we introduce a new approach that circumvents these roadblocks by adapting a genetically-encoded ascorbate peroxidase (APEX2) as a fusion protein to a membrane-targeted fluorescent reporter (CAAX-Venus), and introduce it in single pyramidal neurons in vivo using extremely sparse in utero cortical electroporation (IUCE). This approach allows to perform Correlated Light-SSEM (CoLSSEM) on individual neurons, reconstructing their dendritic and axonal arborization in a targeted way via combination of high-resolution confocal microscopy, and subsequently imaging of its ultrastuctural features and synaptic connections with the ATUM-SEM (automated tape-collecting ultramicrotome - scanning electron microscopy) technology. Our method significantly improves the the feasibility of large-scale reconstructions of neurons within a circuit, and bridges the description of ultrastructural features of genetically-identified neurons with their functional and/or structural connectivity, one of the main goal of connectomics.

neuroscience↗