Living systems process a broad range of internal and external stimuli, respond to environmental constraints, and adapt to various conditions through tight coordination between signaling networks and cellular mechanics. Among these, calcium signaling and cytoskeletal regulation form an essential interplay that spans multiple scales of biological organization-from ion-protein interactions to intercellular communication and tissue-level behaviors. Calcium ions (Ca2+) act as universal messengers, integrating a wide range of cellular signaling inputs to modulate a broad range of cellular structures and functions through the spatiotemporal dynamics of their concentration changes. Ca2+ signals follow conserved principles, despite their diverse roles, that define regulatory "Rules of Life" (RoLs)-generalized mechanisms that operate across biological contexts. This review focuses on how Ca2+ regulates and is regulated by cytoskeletal dynamics, with a particular emphasis on computational modeling for predictive simulations. As key examples, we highlight three specific RoLs: (1) Ca2+ dynamics facilitate cytoskeletal reorganization following stress and damage, (2) Ca2+ regulates actin dynamics to control synapse processes supporting both synapse formation and exocytosis, and (3) reciprocal coupling of spatiotemporal Ca2+ signaling and cellular dynamics defines distinct cellular roles in emergent multicellular behavior. Finally, we outline future directions toward developing multimodal computational simulations for identifying new RoLs, integrating them into multi-scale computational frameworks, and applications in bioengineering, pharmacology, and regenerative medicine.

The G protein alpha subunit, Gαq, transduces extracellular signals from G-protein-coupled receptors (GPCRs) into the cell, playing essential roles in developmental processes such as organ size control, wound healing, and disease. Hyperactivating mutations in the Gαq are associated with Sturge-Weber syndrome and uveal melanoma, and thus, it serves as an important candidate drug target. However, the downstream mechanisms of Gαq signaling remain poorly defined, creating a bottleneck for designing more effective and targeted therapeutics. Here, we used Drosophila melanogaster wing discs to investigate the cellular and transcriptional consequences of Gαq dysregulation in a model epithelial system. We found that overexpression of Gαq in the wing discs reduces adult wing size and induces systemic developmental delay. Additional notable phenotypes include decreased apoptosis and reduced proliferation. Transcriptomic profiling reveals that the JAK/STAT signaling pathway is specifically upregulated in Gαq overexpression, but not in Gαq knockdown. Furthermore, perturbing Gαq impacts the cytoskeleton, confirmed by altered localization of phosphorylated Myosin II. Gαq overexpression in the wing disc upregulates stress-response pathways and triggers secretion of Drosophila insulin-like peptide 8 (Dilp8), a hormone that coordinates growth and developmental timing. Functional experiments confirmed that IP₃ receptor (IP₃R)-dependent calcium signaling mediates this delay and that the delay is rescued by the knockdown of Dilp8. In sum, Gαq acts as a critical regulator of epithelial growth and developmental timing via Ca2+-dependent Dilp8 signaling. These findings establish mechanistic links between GPCR signaling, tissue regeneration, and systemic developmental coordination, with broader implications for understanding Gαq-related pathologies in humans. This study explores how a protein called Gαq helps organs grow to the optimal size and shape during development, using fruit flies as a model. Gαq is part of a signaling system that controls how cells communicate and respond to their environment. We found that Gαq helps produce waves of calcium activity in developing wing tissue. When we altered Gαq levels during larval development, the adult wings became smaller. This was due to fewer cells dividing and, unexpectedly, fewer cells dying. These effects may relate to how Gαq functions in human diseases like cancer, though more research is needed. Gαq also slowed overall development. This delay was linked to the release of a signal called Dilp8, which tells the body to slow down growth so tissues can catch up. We showed that blocking Dilp8, or interfering with calcium signaling, could restore normal development speed. This means Gαq plays a role in managing developmental timing through a hormone system that coordinates growth across the body. Further genetic analysis revealed that Gαq activates several important pathways involved in immunity, growth, and cell structure. It also affects how cells connect physically and multiply, which are crucial for shaping tissues. In summary, Gαq is a key regulator of growth and timing during development. By influencing both local cell behavior and whole-body signals, it ensures that organs form correctly and in sync with the rest of the organism.

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 Summary This 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. ### Competing Interest Statement The authors have declared no competing interest. NSF, 2120200

Mechanosensitive Piezo channels regulate cell division, cell extrusion, and cell death. However, systems-level functions of Piezo in regulating organogenesis remain poorly understood. Here, we demonstrate that Piezo controls epithelial cell topology to ensure precise organ growth by integrating live-imaging experiments with pharmacological and genetic perturbations and computational modeling. Notably, the knockout or knockdown of Piezo increases bilateral asymmetry in wing size. Piezo's multifaceted functions can be deconstructed as either autonomous or non-autonomous based on a comparison between tissue-compartment-level perturbations or between genetic perturbation populations at the whole-tissue level. A computational model that posits cell proliferation and apoptosis regulation through modulation of the cutoff tension required for Piezo channel activation explains key cell and tissue phenotypes arising from perturbations of Piezo expression levels. Our findings demonstrate that Piezo promotes robustness in regulating epithelial topology and is necessary for precise organ size control.

This summary of recent contributions in the Biophysical Journal from 2020 to 2023 highlights new mechanistic insights into key biomechanical and biophysical aspects of neurodegeneration. Neurodegeneration encompasses complex diseases characterized by the progressive loss of neuronal function, often linked to protein accumulation and aggregation. Several factors, including mechanical properties and structural composition of brain tissue, formation of proteinaceous condensates within cells, and protein transport between cells, impact the loss of neural function.

Mechanosensitive Piezo channels regulate cell division through calcium-mediated activation of ERK signaling or activate Rho signaling to mediate cell extrusion and cell death. However, systems-level functions of Piezo in regulating organogenesis remain poorly understood. Here, we demonstrate that Piezo controls epithelial cell topology to ensure precise organ growth through the integration of live imaging experiments with pharmacological and genetic perturbations and computational modeling. Notably, knockout or knockdown of Piezo led to bilateral asymmetry in wing phenotypes. While pharmacological activation of Piezo stimulated an increase in the frequency of spikes in cytosolic Ca2+, we discovered that Piezo overexpression counterintuitively reduces Ca2+ signaling dynamics. Knockdown of Piezo inhibited proliferation and decreased apoptosis, resulting in an overall increase in epithelial overcrowding. In contrast, either genetic overexpression or pharmacological activation of Piezo increased cell proliferation and cell removal through basal extrusion. Surprisingly, Piezo overexpression increased the hexagonality of cellular topology. To test whether Piezo regulates cell topology, we formulated computational simulations to investigate how expression levels of Piezo protein regulate cell proliferation and apoptosis through modulation of the cut-off tension required for Piezo channel activation. Quantitative analysis validated computational simulation predictions of how perturbations to Piezo impacted epithelial topology. Overall, our findings demonstrate that Piezo promotes robustness in regulating epithelial topology and is necessary for precise organ size control.

Background G proteins mediate cell responses to various ligands and play key roles in organ development. Dysregulation of G-proteins or Ca 2+ 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. Methods We employed the Gal4/UAS binary system to inhibit or overexpress Gαq 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 Gαq homeostasis. Results Here, we characterized how the G protein subunit Gαq tunes the size and shape of the wing in the larval and adult stages of development. Downregulation of Gαq in the wing disc reduced wing growth and delayed larval development. Gαq overexpression is sufficient to promote global Ca 2+ 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 Ca 2+ signaling toolkit, suggesting that downstream Ca 2+ signaling partially ameliorates the reduction in wing size. In contrast, Gαq -mediated pupariation delay is rescued by inhibition of IP 3 R, a key regulator of Ca 2+ signaling. This suggests that Gαq regulates developmental phenotypes through both Ca 2+ -dependent and Ca 2+ -independent mechanisms. RNA seq analysis shows that disruption of Gαq homeostasis affects nuclear hormone receptors, JAK/STAT pathway, and immune response genes. Notably, disruption of Gαq homeostasis increases expression levels of Dilp8, a key regulator of growth and pupariation timing. Conclusion Gαq activity contributes to cell size regulation and wing metamorphosis. Disruption to Gαq homeostasis in the peripheral wing disc organ delays larval development through ecdysone signaling inhibition. Overall, Gαq signaling mediates key modules of organ size regulation and epithelial homeostasis through the dual action of Ca 2+ -dependent and independent mechanisms.

Recycling spent lithium-ion batteries (LIBs) could alleviate supply risks for critical metals and be less harmful to the environment compared to new production of metals from mining. Developing a cost-effective LIB bioleaching process could be a promising alternative to traditional energy-intensive recycling technologies. This study aimed to optimize bioleaching conditions for maximum economic competitiveness through design of experiments using iterative response surface methodology (RSM), assisted by thermodynamic modeling. The optimal condition was identified as 2.5% pulp density in 75 mM gluconic acid biolixiviant at 55°C for 30 h which could recover 57%–84% of nickel, 71%–86% of cobalt, and 100% of lithium and manganese, yielding a 17%–26% net profit margin. The recommended pulp density and acid concentrations, together with the observed metal solubilization, were supported by thermodynamic modeling predictions. Our study demonstrated that combining RSM with thermodynamic simulations could be a powerful tool for optimizing bioleaching conditions.

Growing our global economic and environmental focus relies, in part, on our development of a sustainable system to recycle valuable metals. This endeavor to recycle these elements falls within the scope of Idaho National Laboratories (INL) mission to pursue new sustainable energy systems that are competitive. To succeed in this endeavor in not only a low-cost but environmentally safe practice, Gluconobacter oxydans was utilized for its ability to produce a bio-lixiviant known for its critical material leaching abilities. G. oxydans is a rod-shaped, gram negative, acidophilic, and obligately aerobic organism. Unlike many other aerobic organisms, it does not completely oxidize its carbon sources to water and carbon dioxide. Instead it incompletely oxidizes its substrates to aldehydes, ketones and organic acids. Because of this metabolic pathway, it was utilized in a batch reactor setting to produce sufficient amounts of a low-pH bio-lixiviant so that leaching processes could be performed on lithium ion battery cathode powders. Some of these processes included adding different molar ratios of a redox agent to the produced bio-lixiviant, alternating concentrations of lithium ion battery cathode powders, varying leaching time, and changing the temperature each leach was performed at. From this, a biohydrometallurgy process was successfully created for the leaching of cobalt from lithium ion cathode powders This project provided a multitude of laboratory and research experiences that resulted in ample opportunity for professional and personal growth. In addition to this, the INL experience fostered the development of many personal skills and business skills to assist in future career opportunities.