A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids

How cells orchestrate their cellular functions remains a crucial question to unravel how they organize in different patterns. We present a framework based on artificial intelligence to advance the understanding of how cell functions are coordinated spatially and temporally in biological systems. It consists of a hybrid physics-based model that integrates both mechanical interactions and cell functions with a data-driven model that regulates the cellular decision-making process through a deep learning algorithm trained on image data metrics. To illustrate our approach, we used data from 3D cultures of murine pancreatic ductal adenocarcinoma cells (PDAC) grown in Matrigel as tumor organoids. Our approach allowed us to find the underlying principles through which cells activate different cell processes to self-organize in different patterns according to the specific microenvironmental conditions. The framework proposed here expands the tools for simulating biological systems at the cellular level, providing a novel perspective to unravel morphogenetic patterns

Bacterial Footprints in Elastic Pillared Microstructures

Soft substrates decorated with micropillar arrays are known to be sensitive to deflection due to capillary action. In this work, we demonstrate that micropillared epoxy surfaces are sensitive to single drops of bacterial suspensions. The micropillars can show significant deformations upon evaporation, just as capillary action does in soft substrates. The phenomenon has been studied with five bacterial strains: S. epidermidis, L. sakei, P. aeruginosa, E. coli, and B. subtilis. The results reveal that only droplets containing motile microbes with flagella stimulate micropillar bending, which leads to significant distortions and pillar aggregations forming dimers, trimers, and higher order clusters. Such deformation is manifested in characteristic patterns that are left on the microarrayed surface following evaporation and can be easily identified even by the naked eye. Our findings could lay the ground for the design and fabrication of mechanically responsive substrates, sensitive to specific types of microorganisms

A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids

Summary: How cells orchestrate their cellular functions remains a crucial question to unravel how they organize in different patterns. We present a framework based on artificial intelligence to advance the understanding of how cell functions are coordinated spatially and temporally in biological systems. It consists of a hybrid physics-based model that integrates both mechanical interactions and cell functions with a data-driven model that regulates the cellular decision-making process through a deep learning algorithm trained on image data metrics. To illustrate our approach, we used data from 3D cultures of murine pancreatic ductal adenocarcinoma cells (PDAC) grown in Matrigel as tumor organoids. Our approach allowed us to find the underlying principles through which cells activate different cell processes to self-organize in different patterns according to the specific microenvironmental conditions. The framework proposed here expands the tools for simulating biological systems at the cellular level, providing a novel perspective to unravel morphogenetic patterns

A Novel Self-Assembly Strategy for the Fabrication of Nano-Hybrid Satellite Materials with Plasmonically Enhanced Catalytic Activity

The generation of hydrogen from water using light is currently one of the most promising alternative energy sources for humankind but faces significant barriers for large-scale applications due to the low efficiency of existing photo-catalysts. In this work we propose a new route to fabricate nano-hybrid materials able to deliver enhanced photo-catalytic hydrogen evolution, combining within the same nanostructure, a plasmonic antenna nanoparticle and semiconductor quantum dots (QDs). For each stage of our fabrication process we probed the chemical composition of the materials with nanometric spatial resolution, allowing us to demonstrate that the final product is composed of a silver nanoparticle (AgNP) plasmonic core, surrounded by satellite Pt decorated CdS QDs (CdS@Pt), separated by a spacer layer of SiO2 with well-controlled thickness. This new type of photoactive nanomaterial is capable of generating hydrogen when irradiated with visible light, displaying efficiencies 300% higher than the constituting photo-active components. This work may open new avenues for the development of cleaner and more efficient energy sources based on photo-activated hydrogen generation.</jats:p

Temperature and pH Stimuli-Responsive System Delivers Location-Specific Antimicrobial Activity with Natural Products.

Smart materials with controlled stimuli-responsive functions are at the forefront of technological development. In this work, we present a generic strategy that combines simple components, physicochemical responses, and easy fabrication methods to achieve a dual stimuli-responsive system capable of location-specific antimicrobial cargo delivery. The encapsulated system is fabricated by combining a biocompatible inert polymeric matrix of poly(dimethylsiloxane) (PDMS) and a bioactive cargo of saturated fatty acids. We demonstrate the effectiveness of our approach to deliver antimicrobial activity for the model bacteria Escherichia coli. The system responds to two control variables, temperature and pH, delivering two levels of antimicrobial response under distinct combinations of stimuli: one response toward the planktonic media and another response directly at the surface for sessile bacteria. Spatially resolved Raman spectroscopy alongside thermal and structural material analysis reveals that the system not only exhibits ON/OFF states but can also control relocation and targeting of the active cargo toward either the surface or the liquid media, leading to different ON/OFF states for the planktonic and sessile bacteria. The approach proposed herein is technologically simple and scalable, facing low regulatory barriers within the food and healthcare sectors by using approved components and relying on fundamental chemical processes. Our results also provide a proof-of-concept platform for the design and easy fabrication of delivery systems capable of operating as Boolean logic gates, delivering different responses under different environmental conditions

Effect of Local Topography on Cell Division of Staphylococcus spp.

Surface engineering is a promising strategy to limit or prevent the formation of biofilms. The use of topographic cues to influence early stages of biofilm formationn has been explored, yet many fundamental questions remain unanswered. In this work, we develop a topological model supported by direct experimental evidence, which is able to explain the effect of local topography on the fate of bacterial micro-colonies of Staphylococcus spp. We demonstrate how topological memory at the single-cell level, characteristic of this genus of Gram-positive bacteria, can be exploited to influence the architecture of micro-colonies and the average number of surface anchoring points over nano-patterned surfaces, formed by vertically aligned silicon nanowire arrays that can be reliably produced on a commercial scale, providing an excellent platform to investigate the effect of topography on the early stages of Staphylococcus spp. colonisation. The surfaces are not intrinsically antimicrobial, yet they delivered a topography-based bacteriostatic effect and a significant disruption of the local morphology of micro-colonies at the surface. The insights from this work could open new avenues towards designed technologies for biofilm engineering and prevention, based on surface topography

Temperature and pH Stimuli-Responsive System Delivers Location-Specific Antimicrobial Activity with Natural Products

Smart materials with controlled stimuli-responsive functions are at the forefront of technological development. In this work, we present a generic strategy that combines simple components, physicochemical responses, and easy fabrication methods to achieve a dual stimuli-responsive system capable of location-specific antimicrobial cargo delivery. The encapsulated system is fabricated by combining a biocompatible inert polymeric matrix of poly(dimethylsiloxane) (PDMS) and a bioactive cargo of saturated fatty acids. We demonstrate the effectiveness of our approach to deliver antimicrobial activity for the model bacteria Escherichia coli. The system responds to two control variables, temperature and pH, delivering two levels of antimicrobial response under distinct combinations of stimuli: one response toward the planktonic media and another response directly at the surface for sessile bacteria. Spatially resolved Raman spectroscopy alongside thermal and structural material analysis reveals that the system not only exhibits ON/OFF states but can also control relocation and targeting of the active cargo toward either the surface or the liquid media, leading to different ON/OFF states for the planktonic and sessile bacteria. The approach proposed herein is technologically simple and scalable, facing low regulatory barriers within the food and healthcare sectors by using approved components and relying on fundamental chemical processes. Our results also provide a proof-of-concept platform for the design and easy fabrication of delivery systems capable of operating as Boolean logic gates, delivering different responses under different environmental conditions

Ion shuttling between emulsion droplets by crown ether modified gold nanoparticles

Selective unidirectional transport of barium ions between droplets in a water-in-chloroform emulsion is demonstrated. Gold nanoparticles (GNPs) modified with a thiolated crown ether act as barium ion complexing shuttles that carry the ions from one population of droplets (source) to another (target). This process is driven by a steep barium ion concentration gradient between source and target droplets. The concentration of barium ions in the target droplets is kept low at all times by the precipitation of insoluble barium sulfate. A potential role of electrostatically coupled secondary processes that maintain the electroneutrality of the emulsion droplets is discussed. Charging of the GNP metal cores by electron transfer in the presence of the Fe(ii)/Fe(iii) redox couple appears to affect the partitioning of the GNPs between the water droplets and the chloroform phase. Processes have been monitored and studied by optical microscopy, Raman spectroscopy, cryogenic scanning electron microscopy (cryo-SEM) and zeta potential. The shuttle action of the GNPs has further been demonstrated electrochemically in a model system