DSpace Angular :: Browsing by Author "Ravasio, Andrea"

Browsing by Author "Ravasio, Andrea"

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A computational framework for testing hypotheses of the minimal mechanical requirements for cell aggregation using early annual killifish embryogenesis as a model
(FRONTIERS MEDIA SA, 2023) Montenegro-Rojas, Ignacio; Yanez, Guillermo; Skog, Emily; Guerrero-Calvo, Oscar; Andaur-Lobos, Martin; Dolfi, Luca; Cellerino, Alessandro; Cerda, Mauricio; Concha, Miguel L.; Bertocchi, Cristina; Rojas, Nicolas O.; Ravasio, Andrea; Rudge, Timothy J.
Introduction: Deciphering the biological and physical requirements for the outset of multicellularity is limited to few experimental models. The early embryonic development of annual killifish represents an almost unique opportunity to investigate de novo cellular aggregation in a vertebrate model. As an adaptation to seasonal drought, annual killifish employs a unique developmental pattern in which embryogenesis occurs only after undifferentiated embryonic cells have completed epiboly and dispersed in low density on the egg surface. Therefore, the first stage of embryogenesis requires the congregation of embryonic cells at one pole of the egg to form a single aggregate that later gives rise to the embryo proper. This unique process presents an opportunity to dissect the self-organizing principles involved in early organization of embryonic stem cells. Indeed, the physical and biological processes required to form the aggregate of embryonic cells are currently unknown., Methods: Here, we developed an in silico, agent-based biophysical model that allows testing how cell-specific and environmental properties could determine the aggregation dynamics of early Killifish embryogenesis. In a forward engineering approach, we then proceeded to test two hypotheses for cell aggregation (cell-autonomous and a simple taxis model) as a proof of concept of modeling feasibility. In a first approach (cell autonomous system), we considered how intrinsic biophysical properties of the cells such as motility, polarity, density, and the interplay between cell adhesion and contact inhibition of locomotion drive cell aggregation into self-organized clusters. Second, we included guidance of cell migration through a simple taxis mechanism to resemble the activity of an organizing center found in several developmental models., Results: Our numerical simulations showed that random migration combined with low cell-cell adhesion is sufficient to maintain cells in dispersion and that aggregation can indeed arise spontaneously under a limited set of conditions, but, without environmental guidance, the dynamics and resulting structures do not recapitulate in vivo observations., Discussion: Thus, an environmental guidance cue seems to be required for correct execution of early aggregation in early killifish development. However, the nature of this cue (e.g., chemical or mechanical) can only be determined experimentally. Our model provides a predictive tool that could be used to better characterize the process and, importantly, to design informed experimental strategies.
A processing product of the Plasmodium falciparum reticulocyte binding protein RH1 shows a close association with AMA1 during junction formation
(2020) Gunalan, K.; Gao, X. H.; Yap, S. S. L.; Lai, S. K.; Ravasio, Andrea; Ganesan, S.; Li, H. Y.; Preiser, P. R.
Alternative molecular mechanisms for force transmission at adherens junctions via β-catenin-vinculin interaction
(2024) Morales-Camilo, Nicole; Liu, Jingzhun; Ramírez Contador, Manuel José; Canales Salgado, Patricio Andrés; Alegría Fuentes, Juan José; Liu, Xuyao; Ong, Ting Ong; Barrera Rojas, Nelson Patricio; Fierro Huerta, Angélica María; Toyama, Yusuke; Goult, Benjamin; Wang, Yilin; Meng, Yue; Nishimura, Ryosuke; Fong-Ngern, Kedsarin; Low, Christine Siok Lan; Kanchanawong, Pakorn; Yan, Jie; Ravasio, Andrea; Bertocchi, Cristina
Force transmission through adherens junctions (AJs) is crucial for multicellular organization, wound healing and tissue regeneration. Recent studies shed light on the molecular mechanisms of mechanotransduction at the AJs. However, the canonical model fails to explain force transmission when essential proteins of the mechanotransduction module are mutated or missing. Here, we demonstrate that, in absence of α-catenin, β-catenin can directly and functionally interact with vinculin in its open conformation, bearing physiological forces. Furthermore, we found that β-catenin can prevent vinculin autoinhibition in the presence of α-catenin by occupying vinculin´s head-tail interaction site, thus preserving force transmission capability. Taken together, our findings suggest a multi-step force transmission process at AJs, where α-catenin and β-catenin can alternatively and cooperatively interact with vinculin. This can explain the graded responses needed to maintain tissue mechanical homeostasis and, importantly, unveils a force-bearing mechanism involving β-catenin and extended vinculin that can potentially explain the underlying process enabling collective invasion of metastatic cells lacking α-catenin.
Author Correction: Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity
(2020) Ravasio, Andrea; Myaing, Myint Z.; Chia, Shumei; Arora, Aditya; Sathe, Aneesh; Cao, Elaine Yiqun; Bertocchi, Cristina; Sharma, Ankur; Arasi, Bakya; Chung, Vin Yee; Greene, Adrienne C.; Tan, Tuan Zea; Chen, Zhongwen; Ong, Hui Ting; Iyer, N. Gopalakrishna; Huang, Ruby YunJu; DasGupta, Ramanuj; Groves, Jay T.; Viasnoff, Virgile
Cohesive energy and interaction of superparamagnetic aggregates
(2020) Rojas, N.; Cerda, M.; Ravasio, Andrea; Rudge, Timothy
Computational framework based on individual agents to model cell aggregation and collective dynamics
(2024) Montenegro Rojas, Ignacio Tomás; Ravasio, Andrea; Pontificia Universidad Católica de Chile. Escuela de Ingeniería
The study of biological systems has given way to the emergence of novel approaches to understanding the intrinsic complexity of life. In this aspect, mechanobiology has emerged as an interesting and modern new branch of the cellular sciences, using physical and engineering approaches to reverse engineer complex systems from their most basic components. Mathematical and computational models provide a powerful tool for investigating functional components and minimal requirements of biological systems. In this thesis, I present a mathematical theory and a computational model capable of describing the complex behavior of multicellular systems and, particularly, the transition from single cell to collective tissue dynamics. While this is relevant to understand, e.g., epithelial tissue dynamics, wound healing, and cancer progression, here I leverage the robustness and relative simplicity of early killifish development to investigate the minimal requirements for cell aggregation. Briefly, the killifish exhibits a unique developmental pattern where single cells aggregate into a multicellular cluster to initiate gastrulation, making it an ideal animal model for studying aggregation in vivo. Based on observation of the in vivo system, the minimal interactions presented in the system are defined, and mathematical definitions for each one are proposed. Thereafter, a fully integrated mathematical model for multicellular migration and aggregation accounting for cell motion, cellular interactions with the environment, Contact Inhibition of Locomotion (CIL), and specific 3D geometries of the embryonic environment is implemented, in absence or presence of environmental cues providing directionality to the cellular motion (taxis). The CellModeller software was used to solve partial differential equations and as a graphical output simulating cellular dynamics. The results from this model are later analyzed and interpreted. Finally, these results, which have been published in Frontiers in Cell and Developmental Biology are discussed, along with future work and potential applications for these types of in silico studies of complex multicellular systems.
Integrating bioengineering, super-resolution microscopy and mechanobiology in autophagy research: addendum to the guidelines (4th edition)
(2024) Ravasio, Andrea; Klionsky, Daniel J.; Bertocchi, Cristina
Recent key technological developments, such as super-resolution microscopy and microfabrication, enabled investigation of biological processes, including macroautophagy/autophagy, with unprecedented spatiotemporal resolution and control over experimental conditions. Such disruptive innovations deepened our capability to provide mechanistic understandings of the autophagic process and its causes. This addendum aims to expand the guidelines on autophagy in three key directions: optical methods enabling visualization of autophagic machinery beyond the diffraction-limited resolution; bioengineering enabling accurate designs and control over experimental conditions; and theoretical advances in mechanobiology connecting autophagy and mechanical processes of the cell.
Large-scale curvature sensing by directional actin flow drives cellular migration mode switching
(2019) Chen, T.; Callan-Jones, A.; Fedorov, E.; Ravasio, Andrea; Brugues, A. Ong, H.T.; Toyama, Y.; Low, B.C.; Trepat, X.; Shemesh, T.; Voituriez, R.; Ladoux, B.
Mechanical Roles of Vinculin/β-catenin interaction in Adherens Junction
(2019) Bertocchi , Cristina; Ravasio, Andrea; Ong, Hui Ting; Toyama, Yusuke; Kanchanawong, Pakorn
Mechanical force transmission through the adherens junctions (AJs) are highly regulated processes essential for multicellular organization of tissues. AJ proteins such as E-cadherin, α-catenin, and vinculin have been shown to be sensing or bearing mechanical forces being transmitted between the actin cytoskeleton and the intercellular contacts. However, the molecular organization and connectivity of these components remains not well understood. Using a super-resolution microscopy approach, we report that vinculin, once activated, could form a direct structural connection with β-catenin, which can bypass α-catenin, one of the main mechanotransducers in AJs. Direct vinculin/β-catenin interaction is capable of supporting mechanical tension and contributes to the stabilization of the cadherin-catenin complexes. These findings suggest a multi-step model for the force-dependent reinforcement of AJs whereby α-catenin may serve as the initial catalytic activator of vinculin, followed by vinculin translocation to form a direct link between E-cadherin-bound β-catenin and the actin cytoskeleton
Mechanoautophagy: Synergies Between Autophagy and Cell Mechanotransduction at Adhesive Complexes
(FRONTIERS MEDIA SA, 2022) Ravasio, Andrea; Morselli, Eugenia; Bertocchi, Cristina
Cells are exposed and respond to various mechanical forces and physical cues stemming from their environment. This interaction has been seen to differentially regulate various cellular processes for maintenance of homeostasis, of which autophagy represents one of the major players. In addition, autophagy has been suggested to regulate mechanical functions of the cells including their interaction with the environment. In this minireview, we summarize the state of the art of the fascinating interplay between autophagy and the mechanotransduction machinery associated with cell adhesions, that we name center dot Mechanoautophagy center dot
Microfabrication approaches for oral research and clinical dentistry
(2023) Tiozzo-Lyon, Paola; Andrade, Matías; Leiva-Sabadini, Camila; Morales, José; Olivares, Antonia; Ravasio, Andrea; Aguayo Paul, Sebastian Daniel
Currently, there is a variety of laboratory tools and strategies that have been developed to investigate in-vivo processes using in-vitro models. Amongst these, microfabrication represents a disruptive technology that is currently enabling next-generation biomedical research through the development of complex laboratory approaches (e.g., microfluidics), engineering of micrometer scale sensors and actuators (micropillars for traction force microscopy), and the creation of environments mimicking cell, tissue, and organ-specific contexts. Although microfabrication has been around for some time, its application in dental and oral research is still incipient. Nevertheless, in recent years multiple lines of research have emerged that use microfabrication-based approaches for the study of oral diseases and conditions with micro- and nano-scale sensitivities. Furthermore, many investigations are aiming to develop clinically relevant microfabrication-based applications for diagnostics, screening, and oral biomaterial manufacturing. Therefore, the objective of this review is to summarize the current application of microfabrication techniques in oral sciences, both in research and clinics, and to discuss possible future applications of these technologies for in-vitro studies and practical patient care. Initially, this review provides an overview of the most employed microfabrication methods utilized in biomedicine and dentistry. Subsequently, the use of micro- and nano-fabrication approaches in relevant fields of dental research such as endodontic and periodontal regeneration, biomaterials research, dental implantology, oral pathology, and biofilms was discussed. Finally, the current and future uses of microfabrication technology for clinical dentistry and how these approaches may soon be widely available in clinics for the diagnosis, prevention, and treatment of relevant pathologies are presented.
Microfabrication-based engineering of biomimetic dentin-like constructs to simulate dental aging
(2024) Alvarez, Simon; Morales, Jose; Tiozzo-Lyon, Paola; Berrios, Pablo; Barraza, Valentina; Simpson, Kevin; Ravasio, Andrea; Monforte Vila, Xavier; Teuschl-Woller, Andreas; Schuh, Christina M. A. P.; Aguayo, Sebastian
Human dentin is a highly organized dental tissue displaying a complex microarchitecture consisting of micrometer-sized tubules encased in a mineralized type-I collagen matrix. As such, it serves as an important substrate for the adhesion of microbial colonizers and oral biofilm formation in the context of dental caries disease, including root caries in the elderly. Despite this issue, there remains a current lack of effective biomimetic in vitro dentin models that facilitate the study of oral microbial adhesion by considering the surface architecture at the micro- and nanoscales. Therefore, the aim of this study was to develop a novel in vitro microfabricated biomimetic dentin surface that simulates the complex surface microarchitecture of exposed dentin. For this, a combination of soft lithography microfabrication and biomaterial science approaches were employed to construct a micropitted PDMS substrate functionalized with mineralized type-I collagen. These dentin analogs were subsequently glycated with methylglyoxal (MGO) to simulate dentin matrix aging in vitro and analyzed utilizing an interdisciplinary array of techniques including atomic force microscopy (AFM), elemental analysis, and electron microscopy. AFM force-mapping demonstrated that the nanomechanical properties of the biomimetic constructs were within the expected biological parameters, and that mineralization was mostly predominated by hydroxyapatite deposition. Finally, dual-species biofilms of Streptococcus mutans and Candida albicans were grown and characterized on the biofunctionalized PDMS microchips, demonstrating biofilm-specific morphologic characteristics and confirming the suitability of this model for the study of early biofilm formation under controlled conditions. Overall, we expect that this novel biomimetic dentin model could serve as an in vitro platform to study oral biofilm formation or dentin-biomaterial bonding in the laboratory without the need for animal or human tooth samples in the future., Our study aimed to develop a novel in vitro microfabricated biomimetic dentin surface that simulates the complex surface microarchitecture of exposed dentin, as well as age-derived glycation of teeth, for the growth of polymicrobial oral biofilms.
Molecular Insights on Shigellosis: How the Interaction Between Invasin IpaA and Vinculin Hijacks Cellular Mechanotransduction
(2023) Bertocchi , Cristina; Morales, Nicole; Ravasio, Andrea
With 270 million infections annually and nearly half a million death a year, shigellosis is a severe intestinal infection caused by bacteria of the Shigella family. Appearance and spread of drug-resistant strains renewed global concerns for public health and finding novel targets for treatment is fast becoming a priority. To this end, invasins are a potentially good candidate. Also called Ipa(s), which is the short for Invasion Plasmid Antigen, invasins play a key role in mediating bacterial invasion and infection of the host cell. Importantly, they have been reported to hijack inbuilt mechanical capability of the host cells such as cell adhesion and active processes mediated by the actin cytoskeleton to enable bacterial ingress into the host cells. IpaA is an invasin of particular interest as it presents three motifs that mimic vinculin binding sites and thus it allows IpaA to interact with vinculin, which is one of the most critical regulators of cellular and tissue mechanics. Using a mechanobiology point-of-view, we aim to provide an overview of Shigella´s infection mechanism, to highlight recently discovered molecular mechanisms of IpaA/vinculin interaction and to finally discuss their consequences for epithelial cell and tissue mechanical homeostasis that may result in the symptomatic outcomes seen in severe shigellosis.
Nanoscale architecture of cadherin-based cell adhesions.
(2017) Bertocchi, C.; Wang, Y.; Ravasio, Andrea; Hara, Y.; Wu, Y.; Sailov, T.; Baird, M.; Davidson, M. W.; Zaidel Bar, R.; Toyama, Y.; Ladoux, B.; Mege, R. M.; Kanchanawong, P.
Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity
(2020) Ravasio, Andrea; Myaing, M. Z.; Chia, S. M.; Arora, A.; Sathe, A.; Cao, E. Y.; Bertocchi, Cristina; Sharma, A.; Arasi, B.; Chung, V. Y.; Green, A. C.; Tan, T. Z.; Chen, Z. W.; Ong, H. T.; Iyer, N. G.; Huang, R. Y.; DasGupta, R.; Groves, J. T.; Viasnoff, V.
VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks
(BMC, 2023) Gatica, Marilyn; Navarro, Carlos F. F.; Lavado, Alejandro; Reig, German; Pulgar, Eduardo; Llanos, Paula; Haertel, Steffen; Ravasio, Andrea; Bertocchi, Cristina; Concha, Miguel L. L.; Cerda, Mauricio
Motivation Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrates, invertebrates and plants, such as zebrafish, killifish, Drosophila or Marchantia, mainly comprise multilayer tissues, and even if microscopes can reach the needed depth, their geometry hinders the selection and subsequent analysis of the optical volumes of interest. Computational tools to "peel" tissues by removing specific layers and reducing 3D volume into planar images, can critically improve visualization and analysis.Results We developed VolumePeeler, a versatile FIJI plugin for virtual 3D "peeling" of image stacks. The plugin implements spherical and spline surface projections. We applied VolumePeeler to perform peeling in 3D images of spherical embryos, as well as non-spherical tissue layers. The produced images improve the 3D volume visualization and enable analysis and quantification of geometrically challenging microscopy datasets.

Browsing by Author "Ravasio, Andrea"

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