Biology subjects

Rio, R.

Publications and source records attributed to Rio, R..

4 recordsLinked to original sources

bioRxiv2026

A zebrafish leprosy model identifies interferon and plasminogen signaling as survival determinants in mycobacterial infection

Although many genes are associated with leprosy, a skin and nerve infection by Mycobacterium leprae, the function of most of these genes in infection remains unknown. This is partly due to a paucity of animal models that are genetically malleable and recapitulate features of the human disease. Zebrafish, a recent leprosy model, have human-like responses to M. leprae, including macrophage-mediated inflammation and neurodegeneration. We confirm this at the transcriptional level, using RNA sequencing (RNAseq) of chronic M. leprae infection of adult zebrafish. This identified regulated zebrafish orthologs of human leprosy-associated genes, including {beta}- and {gamma}-interferon, IL-6, IL-10, IL-4, and TNF superfamily members. Other regulated genes have not been previously associated with leprosy. Genes associated with tuberculoid leprosy (T-lep) were largely downregulated, while lepromatous leprosy (L-lep) genes were upregulated. Pathways relevant to leprosy, such as phagocytosis and antiviral responses, differed between early and late stages of infection. In infected rag1 mutant zebrafish, which lack T and B cells, T-lep genes were downregulated, suggesting that adaptive immunity is required for their expression. Key pathways and genes were validated by qPCR using zebrafish infection with M. marinum:PGL-1, a model pathogen that can express M. leprae genes. This system allowed for the identification of validated M. leprae-regulated genes that alter infection outcomes, by using multiplex CRISPR to simultaneously mutate many zebrafish genes. 17 genes were screened and 2 were identified that increased mortality infection: isg15 (interferon-stimulated gene 15) and serpine1 (plasminogen activator inhibitor-1). This work confirms that, in humans and zebrafish, type I interferon and plasminogen activation are required for survival of mycobacterial disease, and demonstrates that multiplex CRISPR can identify mediators of host defense in vivo.

microbiology↗

bioRxiv2025

A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods

BackgroundPhagocytosis is a universal physiological process in eukaryotes with many important biological functions. In nudibranch gastropods, a novel form of phagocytosis called nematocyst sequestration is specialized for the uptake of venomous stinging organelles stolen from their cnidarian prey. This process is highly selective. Here we use the emerging model nudibranch species Berghia stephanieae and Hermissenda opalescens to identify genes enriched within the body regions where nematocyst sequestration occurs, and investigate how the expression profile of phagocytosis, immune, and digestive genes differs between nematocyst sequestering regions relative to those where other phagocytic functions occur. ResultsWe identified 166 genes with significantly higher expression in sequestering regions in B. stephanieae, including genes associated with development, membrane transport, and metabolism. Of these, 41 overlap with transcripts upregulated in H. opalescens sequestering tissues. Using Hybridization Chain Reaction in situs, we show that at least two of these genes were localized to sequestering cells in B. stephanieae, including a putative C-type lectin receptor and a collagen. Genes annotated with phagocytosis, digestion, or immunity GO terms were often expressed in both sequestering and non-sequestering tissues, suggesting that they may also play a role in sequestration processes. ConclusionOur results suggest that phagocytosis genes likely play a role in the sequestration phenotype, and that a small subset of genes (e.g., collagen) may play unique functions yet to be uncovered. However, we also show that genes categorized in GO terms related to endocytosis, immunity, and digestion show a clear decrease in overall expression in sequestering tissues. This study lays the foundation for further inquiry into mechanisms of organelle sequestration in nudibranchs and other organisms.

evolutionary biology↗

bioRxiv2024

A genetic and microscopy toolkit for live imaging of whole-body regeneration in Macrostomum lignano

Live imaging of regenerative processes can reveal how animals restore their bodies after injury through a cascade of dynamic cellular events. Here, we present a comprehensive toolkit for live imaging of whole-body regeneration in the flatworm Macrostomum lignano, including a high throughput cloning pipeline, targeted cellular ablation, and advanced microscopy solutions. Using tissue-specific reporter expression, we examine how various structures regenerate. Enabled by a custom, low-cost luminescence/fluorescence microscope, we overcome intense stress-induced autofluorescence to demonstrate the first application of genetic cellular ablation in flatworms to reveal the limited regenerative capacity of neurons and their essential role during wound-healing. Finally, we build a novel open-source tracking microscope to continuously image moving animals throughout the week-long process of regeneration, quantifying kinetics of wound healing, nerve cord repair, body regeneration, growth, and behavioral recovery. Our findings suggest that nerve cord reconnection operates independently from primary body axis re-establishment and other downstream regenerative processes.

bioengineering↗

bioRxiv2019

The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

BackgroundTsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

genomics↗