Gazzo, D. | bioRxiv Science

bioRxiv2025

CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals

Fluctuations and propagation of cytosolic calcium levels at both the cellular and tissue levels show complex patterns, referred to as calcium signatures, that regulate growth, organ development, damage responses, and survival. The quantitative analysis of calcium signatures at the cellular level is essential for identifying unique patterns that coordinate biological processes. However, a versatile framework applicable to multiple tissue types, allowing researchers to compare, measure, and validate diverse responses and recognize conserved patterns across model organisms, is missing. Here, we present a post-processing tool, CalciumInsights, which leverages the R packages Shiny and Golem. This tool has a graphical user interface and does not require software programming experience to perform calcium signal analysis. The open-source software has a modular framework with standardized functionalities that can be tailored for various research approaches. CalciumInsights provides descriptive statistical analysis through various metrics extracted from dynamic calcium transients and oscillations, such as peak amplitude, area under the curve, frequency, among others. The tool was evaluated with fluorescence imaging data from three model organisms: Danio rerio, Arabidopsis thaliana, and Drosophila melanogaster, demonstrating its ability to analyze diverse biological responses and models. Finally, the open-source nature of CalciumInsights enables community-driven improvements and developments for enabling new applications. Author SummaryThis manuscript introduces CalciumInsights, an open-source tool for calcium signature analysis. Designed to be a versatile tool that works with various tissue types and biological systems, CalciumInsights has an easy-to-use graphical user interface. Our program simplifies metrics extraction while maintaining the quality of the analysis by integrating several algorithms. CalciumInsights stands out for its user-friendliness, ease of use, and robust data exploration features, such as tunable filters for improved accuracy. These features promote inclusivity and lower barriers to scientific research by making calcium signature analysis accessible to users of all programming skill levels.

bioengineering↗

bioRxiv2023

The multimodal action of G alpha q in coordinating growth and homeostasis in the Drosophila wing imaginal disc

BackgroundG proteins mediate cell responses to various ligands and play key roles in organ development. Dysregulation of G-proteins or Ca2+ signaling impacts many human diseases and results in birth defects. However, the downstream effectors of specific G proteins in developmental regulatory networks are still poorly understood. MethodsWe employed the Gal4/UAS binary system to inhibit or overexpress Gq in the wing disc, followed by phenotypic analysis. Immunohistochemistry and next-gen RNA sequencing identified the downstream effectors and the signaling cascades affected by the disruption of Gq homeostasis. ResultsHere, we characterized how the G protein subunit Gq tunes the size and shape of the wing in the larval and adult stages of development. Downregulation of Gq in the wing disc reduced wing growth and delayed larval development. Gq overexpression is sufficient to promote global Ca2+ waves in the wing disc with a concomitant reduction in the Drosophila final wing size and a delay in pupariation. The reduced wing size phenotype is further enhanced when downregulating downstream components of the core Ca2+ signaling toolkit, suggesting that downstream Ca2+ signaling partially ameliorates the reduction in wing size. In contrast, Gq-mediated pupariation delay is rescued by inhibition of IP3R, a key regulator of Ca2+ signaling. This suggests that Gq regulates developmental phenotypes through both Ca2+-dependent and Ca2+-independent mechanisms. RNA seq analysis shows that disruption of Gq homeostasis affects nuclear hormone receptors, JAK/STAT pathway, and immune response genes. Notably, disruption of Gq homeostasis increases expression levels of Dilp8, a key regulator of growth and pupariation timing. ConclusionGq activity contributes to cell size regulation and wing metamorphosis. Disruption to Gq homeostasis in the peripheral wing disc organ delays larval development through ecdysone signaling inhibition. Overall, Gq signaling mediates key modules of organ size regulation and epithelial homeostasis through the dual action of Ca2+-dependent and independent mechanisms.

developmental biology↗