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Blondel M, Machet C, Wildemann B, Abidine Y, Swider P. Mechanobiology of bacterial biofilms: Implications for orthopedic infection. J Orthop Res 2024; 42:1861-1869. [PMID: 38432991 DOI: 10.1002/jor.25822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Postoperative bacterial infections are prevalent complications in both human and veterinary orthopedic surgery, particularly when a biofilm develops. These infections often result in delayed healing, early revision, permanent functional loss, and, in severe cases, amputation. The diagnosis and treatment pose significant challenges, and bacterial biofilm further amplifies the therapeutic difficulty as it confers protection against the host immune system and against antibiotics which are usually administered as a first-line therapeutic option. However, the inappropriate use of antibiotics has led to the emergence of numerous multidrug-resistant organisms, which largely compromise the already imperfect treatment efficiency. In this context, the study of bacterial biofilm formation allows to better target antibiotic use and to evaluate alternative therapeutic strategies. Exploration of the roles played by mechanical factors on biofilm development is of particular interest, especially because cartilage and bone tissues are reactive environments that are subjected to mechanical load. This review delves into the current landscape of biofilm mechanobiology, exploring the role of mechanical factors on biofilm development through a multiscale prism starting from bacterial microscopic scale to reach biofilm mesoscopic size and finally the macroscopic scale of the fracture site or bone-implant interface.
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Affiliation(s)
- Margaux Blondel
- Small Animal Surgery Department, Lyon University, VetAgro Sup, Marcy l'Etoile, France
| | - Camille Machet
- National Veterinary School of Toulouse, Toulouse, France
| | - Britt Wildemann
- Experimental Trauma Surgery, Department of Trauma, Hand and Reconstructive Surgery, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Yara Abidine
- Institut de Mécanique des Fluides (IMFT), CNRS & Toulouse University, Toulouse, France
| | - Pascal Swider
- Institut de Mécanique des Fluides (IMFT), CNRS & Toulouse University, Toulouse, France
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2
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Azulay H, Benyunes I, Elber G, Qvit N. Studying Biomolecular Protein Complexes via Origami and 3D-Printed Models. Int J Mol Sci 2024; 25:8271. [PMID: 39125840 PMCID: PMC11311606 DOI: 10.3390/ijms25158271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Living organisms are constructed from proteins that assemble into biomolecular complexes, each with a unique shape and function. Our knowledge about the structure-activity relationship of these complexes is still limited, mainly because of their small size, complex structure, fast processes, and changing environment. Furthermore, the constraints of current microscopic tools and the difficulty in applying molecular dynamic simulations to capture the dynamic response of biomolecular complexes and long-term phenomena call for new supplementary tools and approaches that can help bridge this gap. In this paper, we present an approach to comparing biomolecular and origami hierarchical structures and apply it to comparing bacterial microcompartments (BMCs) with spiral-based origami models. Our first analysis compares proteins that assemble the BMC with an origami model called "flasher", which is the unit cell of an assembled origami model. Then, the BMC structure is compared with the assembled origami model and based on the similarity, a physical scaled-up origami model, which is analogous to the BMC, is constructed. The origami model is translated into a computer-aided design model and manufactured via 3D-printing technology. Finite element analysis and physical experiments of the origami model and 3D-printed parts reveal trends in the mechanical response of the icosahedron, which is constructed from tiled-chiral elements. The chiral elements rotate as the icosahedron expands and we deduce that it allows the BMC to open gates for transmembrane passage of materials.
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Affiliation(s)
- Hay Azulay
- Independent Researcher, Koranit 2018100, Israel;
| | - Inbar Benyunes
- Faculty of Mechanical Engineering, Technion IIT, Haifa 3200003, Israel;
| | - Gershon Elber
- Faculty of Computer Science, Technion IIT, Haifa 3200003, Israel;
| | - Nir Qvit
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed 1311502, Israel
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3
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Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Holler C, Taylor RW, Schambony A, Möckl L, Sandoghdar V. A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control. Nat Methods 2024; 21:512-520. [PMID: 38347139 PMCID: PMC10927540 DOI: 10.1038/s41592-024-02177-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/08/2024] [Indexed: 03/13/2024]
Abstract
Delivery of very small amounts of reagents to the near-field of cells with micrometer spatial precision and millisecond time resolution is currently out of reach. Here we present μkiss as a micropipette-based scheme for brushing a layer of small molecules and nanoparticles onto the live cell membrane from a subfemtoliter confined volume of a perfusion flow. We characterize our system through both experiments and modeling, and find excellent agreement. We demonstrate several applications that benefit from a controlled brush delivery, such as a direct means to quantify local and long-range membrane mobility and organization as well as dynamical probing of intercellular force signaling.
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Affiliation(s)
- Cornelia Holler
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Richard William Taylor
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Alexandra Schambony
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Leonhard Möckl
- Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.
- Department of Physics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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5
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Kerivan EM, Amari VN, Weeks WB, Hardin LH, Tobin L, Azzam OYA, Reinemann DN. Deciphering Mechanochemical Influences of Emergent Actomyosin Crosstalk using QCM-D. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582155. [PMID: 38464072 PMCID: PMC10925119 DOI: 10.1101/2024.02.26.582155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Cytoskeletal protein ensembles exhibit emergent mechanics where behavior exhibited in teams is not necessarily the sum of the components' single molecule properties. In addition, filaments may act as force sensors that distribute feedback and influence motor protein behavior. To understand the design principles of such emergent mechanics, we developed an approach utilizing QCM-D to measure how actomyosin bundles respond mechanically to environmental variables that alter constituent myosin II motor behavior. We demonstrate that QCM-D can detect changes in actomyosin viscoelasticity due to molecular-level alterations, such as motor concentration and nucleotide state, thus providing evidence for actin's role as a mechanical force-feedback sensor and a new approach for deciphering the fundamental mechanisms of emergent cytoskeletal ensemble crosstalk. Justification Cytoskeletal ensembles exhibit mechanics that are not necessarily the sum of the components' single molecule properties, and this emergent behavior is not well understood. Cytoskeletal filaments may also act as force sensors that influence constituent motor protein behavior. To understand the elusive design principles of such emergent mechanics, we innovated an approach using QCM-D to measure how actomyosin bundles sense and respond mechanically to environmental variables. We demonstrate for the first time that QCM-D can detect changes in actomyosin viscoelasticity due to molecular-level alterations, thus providing evidence for actin's role as a mechanical force-feedback sensor and a new approach for deciphering the fundamentals of emergent cytoskeletal ensemble crosstalk.
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6
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Jacob MS. Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems. Biosystems 2023:104939. [PMID: 37295595 DOI: 10.1016/j.biosystems.2023.104939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
What is an organism? In the absence of a fundamental biological definition, what constitutes a living organism, whether it is a unicellular microbe, a multicellular being or a multi-organismal society, remains an open question. New models of living systems are needed to address the scale of this question, with implications for the relationship between humanity and planetary ecology. Here we develop a generic model of an organism that can be applied across multiple scales and through major evolutionary transitions to form a toolkit, or bio-organon, for theoretical studies of planetary-wide physiology. The tool identifies the following core organismic principles that cut across spatial scale: (1) evolvability through self-knowledge, (2) entanglement between energy and information, and (3) extrasomatic "technology" to scaffold increases in spatial scale. Living systems are generally defined by their ability to self-sustain against entropic forces of degradation. Life "knows" how to survive from the inside, not from its genetic code alone, but by utilizing this code through dynamically embodied and functionally specialized flows of information and energy. That is, entangled metabolic and communication networks bring encoded knowledge to life in order to sustain life. However, knowledge is itself evolved and is evolving. The functional coupling between knowledge, energy and information has ancient origins, enabling the original, cellular "biotechnology," and cumulative evolutionary creativity in biochemical products and forms. Cellular biotechnology also enabled the nesting of specialized cells into multicellular organisms. This nested organismal hierarchy can be extended further, suggesting that an organism of organisms, or a human "superorganism," is not only possible, but in keeping with evolutionary trends.
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Affiliation(s)
- Michael S Jacob
- Human Energy, 21 Orinda Way, Suite C 208, Orinda, CA, 94563, United States; Mental Health Service, San Francisco VA Medical Center, 4150 Clement St, San Francisco, CA, 94121, United States; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, 505 Parnassus Ave, San Francisco, CA, 94143, United States.
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7
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Kerivan EM, Tobin L, Basil M, Reinemann DN. Molecular and cellular level characterization of cytoskeletal mechanics using a quartz crystal microbalance. Cytoskeleton (Hoboken) 2023; 80:100-111. [PMID: 36891731 PMCID: PMC10272097 DOI: 10.1002/cm.21752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/19/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023]
Abstract
A quartz crystal microbalance (QCM) is an instrument that has the ability to measure nanogram-level changes in mass on a quartz sensor and is traditionally used to probe surface interactions and assembly kinetics of synthetic systems. The addition of dissipation monitoring (QCM-D) facilitates the study of viscoelastic systems, such as those relevant to molecular and cellular mechanics. Due to real-time recording of frequency and dissipation changes and single protein-level precision, the QCM-D is effective in interrogating the viscoelastic properties of cell surfaces and in vitro cellular components. However, few studies focus on the application of this instrument to cytoskeletal systems, whose dynamic parts create interesting emergent mechanics as ensembles that drive essential tasks, such as division and motility. Here, we review the ability of the QCM-D to characterize key kinetic and mechanical features of the cytoskeleton through in vitro reconstitution and cellular assays and outline how QCM-D studies can yield insightful mechanical data alone and in tandem with other biophysical characterization techniques.
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Affiliation(s)
- Emily M. Kerivan
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677 USA
| | - Lyle Tobin
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677 USA
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677 USA
| | - Mihir Basil
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677 USA
| | - Dana N. Reinemann
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677 USA
- Department of Chemical Engineering, University of Mississippi, University, MS 38677 USA
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8
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Savoie W, Tuazon H, Tiwari I, Bhamla MS, Goldman DI. Amorphous entangled active matter. SOFT MATTER 2023; 19:1952-1965. [PMID: 36809295 PMCID: PMC11164134 DOI: 10.1039/d2sm01573k] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of amorphous entangled systems, specifically from soft and active materials, has the potential to open exciting new classes of active, shape-shifting, and task-capable 'smart' materials. However, the global emergent mechanics that arise from the local interactions of individual particles are not well understood. In this study, we examine the emergent properties of amorphous entangled systems in an in silico collection of u-shaped particles ("smarticles") and in living entangled aggregate of worm blobs (L. variegatus). In simulations, we examine how material properties change for a collective composed of smarticles as they undergo different forcing protocols. We compare three methods of controlling entanglement in the collective: external oscillations of the ensemble, sudden shape-changes of all individuals, and sustained internal oscillations of all individuals. We find that large-amplitude changes of the particle's shape using the shape-change procedure produce the largest average number of entanglements, with respect to the aspect ratio (l/w), thus improving the tensile strength of the collective. We demonstrate applications of these simulations by showing how the individual worm activity in a blob can be controlled through the ambient dissolved oxygen in water, leading to complex emergent properties of the living entangled collective, such as solid-like entanglement and tumbling. Our work reveals principles by which future shape-modulating, potentially soft robotic systems may dynamically alter their material properties, advancing our understanding of living entangled materials, while inspiring new classes of synthetic emergent super-materials.
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Affiliation(s)
- William Savoie
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - Daniel I Goldman
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30318, USA
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9
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Rodríguez-Galván A, Contreras-Torres FF. Scanning Tunneling Microscopy of Biological Structures: An Elusive Goal for Many Years. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3013. [PMID: 36080050 PMCID: PMC9457988 DOI: 10.3390/nano12173013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Scanning tunneling microscopy (STM) is a technique that can be used to directly observe individual biomolecules at near-molecular scale. Within this framework, STM is of crucial significance because of its role in the structural analysis, the understanding the imaging formation, and the development of relative techniques. Four decades after its invention, it is pertinent to ask how much of the early dream has come true. In this study, we aim to overview different analyses for DNA, lipids, proteins, and carbohydrates. The relevance of STM imaging is exhibited as an opportunity to assist measurements and biomolecular identification in nanobiotechnology, nanomedicine, biosensing, and other cutting-edge applications. We believe STM research is still an entire science research ecosystem for joining several areas of expertise towards a goal settlement that has been elusive for many years.
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Affiliation(s)
- Andrés Rodríguez-Galván
- Carrera de Biología, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edo. Mex., Mexico
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10
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Català-Castro F, Schäffer E, Krieg M. Exploring cell and tissue mechanics with optical tweezers. J Cell Sci 2022; 135:jcs259355. [PMID: 35942913 DOI: 10.1242/jcs.259355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellular and tissue biosystems emerge from the assembly of their constituent molecules and obtain a set of specific material properties. To measure these properties and understand how they influence cellular function is a central goal of mechanobiology. From a bottoms-up, physics or engineering point-of-view, such systems are a composition of basic mechanical elements. However, the sheer number and dynamic complexity of them, including active molecular machines and their emergent properties, makes it currently intractable to calculate how biosystems respond to forces. Because many diseases result from an aberrant mechanotransduction, it is thus essential to measure this response. Recent advances in the technology of optical tweezers have broadened their scope from single-molecule applications to measurements inside complex cellular environments, even within tissues and animals. Here, we summarize the basic optical trapping principles, implementations and calibration procedures that enable force measurements using optical tweezers directly inside cells of living animals, in combination with complementary techniques. We review their versatility to manipulate subcellular organelles and measure cellular frequency-dependent mechanics in the piconewton force range from microseconds to hours. As an outlook, we address future challenges to fully unlock the potential of optical tweezers for mechanobiology.
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Affiliation(s)
- Frederic Català-Castro
- Neurophotonics and Mechanical Systems Biology, ICFO, Institut de Ciències Fotòniques, 08860 Castelldefels, Spain
| | - Erik Schäffer
- Cellular Nanoscience, ZMBP, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Krieg
- Neurophotonics and Mechanical Systems Biology, ICFO, Institut de Ciències Fotòniques, 08860 Castelldefels, Spain
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11
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Efremov YM, Suter DM, Timashev PS, Raman A. 3D nanomechanical mapping of subcellular and sub-nuclear structures of living cells by multi-harmonic AFM with long-tip microcantilevers. Sci Rep 2022; 12:529. [PMID: 35017598 PMCID: PMC8752865 DOI: 10.1038/s41598-021-04443-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Recent developments such as multi-harmonic Atomic Force Microscopy (AFM) techniques have enabled fast, quantitative mapping of nanomechanical properties of living cells. Due to their high spatiotemporal resolution, these methods provide new insights into changes of mechanical properties of subcellular structures due to disease or drug response. Here, we propose three new improvements to significantly improve the resolution, identification, and mechanical property quantification of sub-cellular and sub-nuclear structures using multi-harmonic AFM on living cells. First, microcantilever tips are streamlined using long-carbon tips to minimize long-range hydrodynamic interactions with the cell surface, to enhance the spatial resolution of nanomechanical maps and minimize hydrodynamic artifacts. Second, simultaneous Spinning Disk Confocal Microscopy (SDC) with live-cell fluorescent markers enables the unambiguous correlation between observed heterogeneities in nanomechanical maps with subcellular structures. Third, computational approaches are then used to estimate the mechanical properties of sub-nuclear structures. Results are demonstrated on living NIH 3T3 fibroblasts and breast cancer MDA-MB-231 cells, where properties of nucleoli, a deep intracellular structure, were assessed. The integrated approach opens the door to study the mechanobiology of sub-cellular structures during disease or drug response.
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Affiliation(s)
- Yuri M Efremov
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
- World-Class Research Center "Digital Biodesign and Personalized Healthcare, Moscow, Russia
| | - Daniel M Suter
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, West Lafayette, IN, USA
| | - Peter S Timashev
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
- World-Class Research Center "Digital Biodesign and Personalized Healthcare, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | - Arvind Raman
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.
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12
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Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021; 13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.
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Affiliation(s)
- Sébastien Lyonnais
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Centre d’Etudes des Maladies Infectieuses et Pharmacologie Anti-Infectieuse (CEMIPAI), CNRS UAR 3725, Université de Montpellier, 1919 Route de Mende, CEDEX 05, 34293 Montpellier, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - S. Kashif Sadiq
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - Cristina Lorca-Oró
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Laure Dufau
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Sara Nieto-Marquez
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Tuixent Escribà
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Natalia Gabrielli
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Xiao Tan
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Mohamed Ouizougun-Oubari
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Josephine Okoronkwo
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Michèle Reboud-Ravaux
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - José Maria Gatell
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Facultat de Medicina y Ciencias de la Salud, Universitat de Barcelona, Carrer de Casanova 143, 08036 Barcelona, Spain
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
| | - Carine Tisné
- Expression Génétique Microbienne, CNRS UMR 8261, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Gilles Mirambeau
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biologie Intégrative des Organismes Marins (BIOM), CNRS UMR 7232, Observatoire Océanologique de Banyuls (OOB), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
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13
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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021. [PMID: 34584211 DOI: 10.1101/2020.10.03.322354v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA
- The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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14
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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021; 4:1136. [PMID: 34584211 PMCID: PMC8478941 DOI: 10.1038/s42003-021-02653-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers. By encapsulating proteins in giant unilamellar vesicles, Bashirzadeh et al find that actin crosslinkers, α-actinin and fascin, can self-assemble with actin into complex structures that depend on the degree of confinement. Further analysis and modeling show that α-actinin and fascin sort to separate domains of these structures. These insights may be generalizable to other biopolymer networks containing crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.,The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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15
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Partain BD, Zhang Q, Unni M, Aldrich J, Rinaldi-Ramos CM, Narayanan S, Allen KD. Spatially-resolved nanometer-scale measurement of cartilage extracellular matrix mobility. Osteoarthritis Cartilage 2021; 29:1351-1361. [PMID: 34052396 PMCID: PMC8543368 DOI: 10.1016/j.joca.2021.05.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Tissues have complex structures, comprised of solid and fluid phases. Improved understanding of interactions between joint fluid and extracellular matrix (ECM) is required in models of cartilage mechanics. X-ray photon correlation spectroscopy (XPCS) directly measures nanometer-scale dynamics and can provide insight into biofluid-biosolid interactions in cartilage. This study applies XPCS to evaluate dynamic interactions between intact cartilage and biofluids. DESIGN Cartilage biopsies were collected from bovine femoral condyles. During XPCS measurements, cartilage samples were exposed to different fluids: deionized water, PBS, synovial fluid, or sonicated synovial fluid. ECM-biofluid interactions were also assessed at different length scales and different depths from the cartilage surface. RESULTS Using XPCS, cartilage ECM mobility was detected at length scales from 50 to 207 nm. As length scale decreased, time scale for autocorrelation decay decreased, suggesting smaller ECM components are more mobile. ECM dynamics were slowed by dehydrating the sample, demonstrating XPCS assesses matrix mobility in hydrated environments. At all length scales, the matrix was more mobile in deionized water and slowest in synovial fluid. Using the 207 nm length scale assessment, ECM dynamics in synovial fluid were fastest at the cartilage surface and progressively slowed as depth into the sample increased, demonstrating XPCS can assess spatial distribution of ECM dynamics. Finally, ECM mobility increased for degraded synovial fluid. CONCLUSIONS This study demonstrates the potential of XPCS to provide unique insights into nanometer-scale cartilage ECM mobility in a spatially resolved manner and illustrates the importance of biosolid-biofluid interactions in dictating ECM dynamics.
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Affiliation(s)
- B D Partain
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Q Zhang
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - M Unni
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - J Aldrich
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - C M Rinaldi-Ramos
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA; Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - S Narayanan
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - K D Allen
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA; Department of Orthopaedics and Rehabilitation, University of Florida, Gainesville, FL, USA.
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16
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Li MI, Xu X, Xi N, Wang W, Xing X, Liu L. Multiparametric atomic force microscopy imaging of single native exosomes. Acta Biochim Biophys Sin (Shanghai) 2021; 53:385-388. [PMID: 33399205 DOI: 10.1093/abbs/gmaa172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M i Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinning Xu
- Cancer Hospital of China Medical University, Shenyang 110042, China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, China
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Wenxue Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojing Xing
- Cancer Hospital of China Medical University, Shenyang 110042, China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Li M, Xi N, Wang YC, Liu LQ. Atomic force microscopy for revealing micro/nanoscale mechanics in tumor metastasis: from single cells to microenvironmental cues. Acta Pharmacol Sin 2021; 42:323-339. [PMID: 32807839 PMCID: PMC8027022 DOI: 10.1038/s41401-020-0494-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanics are intrinsic properties which appears throughout the formation, development, and aging processes of biological systems. Mechanics have been shown to play important roles in regulating the development and metastasis of tumors, and understanding tumor mechanics has emerged as a promising way to reveal the underlying mechanisms guiding tumor behaviors. In particular, tumors are highly complex diseases associated with multifaceted factors, including alterations in cancerous cells, tissues, and organs as well as microenvironmental cues, indicating that investigating tumor mechanics on multiple levels is significantly helpful for comprehensively understanding the effects of mechanics on tumor progression. Recently, diverse techniques have been developed for probing the mechanics of tumors, among which atomic force microscopy (AFM) has appeared as an excellent platform enabling simultaneously characterizing the structures and mechanical properties of living biological systems ranging from individual molecules and cells to tissue samples with unprecedented spatiotemporal resolution, offering novel possibilities for understanding tumor physics and contributing much to the studies of cancer. In this review, we survey the recent progress that has been achieved with the use of AFM for revealing micro/nanoscale mechanics in tumor development and metastasis. Challenges and future progress are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong, China
| | - Yue-Chao Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lian-Qing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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18
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Fritzsche M. What Is the Right Mechanical Readout for Understanding the Mechanobiology of the Immune Response? Front Cell Dev Biol 2021; 9:612539. [PMID: 33718355 PMCID: PMC7946994 DOI: 10.3389/fcell.2021.612539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/02/2021] [Indexed: 01/06/2023] Open
Affiliation(s)
- Marco Fritzsche
- Rosalind Franklin Institute, Didcot, United Kingdom.,Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
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19
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Fülöp T, Desroches M, A Cohen A, Santos FAN, Rodrigues S. Why we should use topological data analysis in ageing: Towards defining the “topological shape of ageing”. Mech Ageing Dev 2020; 192:111390. [DOI: 10.1016/j.mad.2020.111390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022]
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20
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Chowdhury D, Ghanti D. Soft mechano-chemistry of molecular hubs in mitotic spindle: biomechanics and mechanical proofreading at microtubule ends. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:284001. [PMID: 32133984 DOI: 10.1088/1361-648x/ab7cc5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A microtubule (MT) is a long stiff tube-shaped filament formed by a hierarchical organization of a large number of tubulin protein molecules. These filaments constitute a major structural component of the scaffold of a multi-component macromolecular machine called mitotic spindle. The plus ends of the MTs are tethered to some specific binding partners by molecular tethers while those of some others are crosslinked by crosslinking molecules. Because of the non-covalent binding involved in the tethering and crosslinking, the attachments formed are intrinsically 'soft'. These attachments are transient because these can get ruptured spontaneously by thermal fluctuations. By implementing in silico the standard protocols of in vitro molecular force spectroscopy, we compute the lifetimes of simple theoretical models of these attachments. The mean lifetime is essentially a mean first-passage time. The stability of cross-linked antiparallel MTs is shown to decrease monotonically with increasing tension, a characteristic of all 'slip-bonds'. This is in sharp contrast to the nonmonotonic variation of the mean lifetime with tension, a mechanical fingerprint of 'catch-bonds', displayed by the MTs tethered to two distinct binding partners. We mention plausible functional implications of these observations in the context of mechanical proofreading.
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21
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Abstract
The cell-free molecular synthesis of biochemical systems is a rapidly growing field of research. Advances in the Human Genome Project, DNA synthesis, and other technologies have allowed the in vitro construction of biochemical systems, termed cell-free biology, to emerge as an exciting domain of bioengineering. Cell-free biology ranges from the molecular to the cell-population scales, using an ever-expanding variety of experimental platforms and toolboxes. In this review, we discuss the ongoing efforts undertaken in the three major classes of cell-free biology methodologies, namely protein-based, nucleic acids–based, and cell-free transcription–translation systems, and provide our perspectives on the current challenges as well as the major goals in each of the subfields.
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Affiliation(s)
- Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Allen P. Liu
- Departments of Mechanical Engineering, Biomedical Engineering, Biophysics, and the Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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22
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Ross TD, Lee HJ, Qu Z, Banks RA, Phillips R, Thomson M. Controlling organization and forces in active matter through optically defined boundaries. Nature 2019; 572:224-229. [PMID: 31391558 PMCID: PMC6719720 DOI: 10.1038/s41586-019-1447-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022]
Abstract
Living systems are capable of locomotion, reconfiguration and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, 'active' molecules that create and manipulate non-equilibrium structures and force fields of up to millimetre length scales1-3. Experimental active-matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures4,5 and generating global flows6-9. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here we uncover non-equilibrium phenomena and principles of boundary-mediated control by optically modulating structures and fluid flow in an engineered system of active biomolecules. Our system consists of purified microtubules and light-activatable motor proteins that crosslink and organize the microtubules into distinct structures upon illumination. We develop basic operations-defined as sets of light patterns-to create, move and merge the microtubule structures. By combining these operations, we create microtubule networks that span several hundred micrometres in length and contract at speeds up to an order of magnitude higher than the speed of an individual motor protein. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control that we uncover may be used to study emergent cellular structures and forces and to develop programmable active-matter devices.
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Affiliation(s)
- Tyler D Ross
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Heun Jin Lee
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
| | - Zijie Qu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rachel A Banks
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, California Institute of Technology, Pasadena, CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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23
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Is the cell really a machine? J Theor Biol 2019; 477:108-126. [PMID: 31173758 DOI: 10.1016/j.jtbi.2019.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 05/06/2019] [Accepted: 06/03/2019] [Indexed: 01/03/2023]
Abstract
It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.
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24
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Satterwhite-Warden JE, Kondepudi DK, Dixon JA, Rusling JF. Thermal- and Magnetic-Sensitive Particle Flocking Motion at the Air–Water Interface. J Phys Chem B 2019; 123:3832-3840. [DOI: 10.1021/acs.jpcb.9b00414] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer E. Satterwhite-Warden
- Department of Chemistry (U-3060), University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Dilip K. Kondepudi
- Department of Chemistry, Wake Forest University, Salem Hall, Box
7486, Winston-Salem, North Carolina 27109, United States
| | - James A. Dixon
- Center for the Ecological Study of Perception & Action: (U-1020), University of Connecticut, 406 Babbidge Road, Storrs, Connecticut 06269, United States
- Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - James F. Rusling
- Department of Chemistry (U-3060), University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
- Department of Surgery and Neag Cancer Center, University of Connecticut Health Center, Farmington, Connecticut 06032, United States
- School of Chemistry, National University of Ireland, Galway, University Road, Galway H91 TK33, Ireland
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25
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Design and Fabrication by Thermal Imprint Lithography and Mechanical Characterization of a Ring-Based PDMS Soft Probe for Sensing and Actuating Forces in Biological Systems. Polymers (Basel) 2019; 11:polym11030424. [PMID: 30960408 PMCID: PMC6473920 DOI: 10.3390/polym11030424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
In this paper, the design, fabrication and mechanical characterization of a novel polydimethylsiloxane (PDMS) soft probe for delivering and sensing forces in biological systems is proposed. On the basis of preliminary finite element (FEM) analysis, the design takes advantage of a suitable core geometry, characterized by a variable spring-like ring. The compliance of probes can be finely set in a wide range to measure forces in the micronewton to nanonewton range. In particular, this is accomplished by properly resizing the ring geometry and/or exploiting the mixing ratio-based elastic properties of PDMS. Fabrication by the thermal imprint lithography method allows fast and accurate tuning of ring sizes and tailoring of the contact section to their targets. By only varying geometrical parameters, the stiffness ranges from 1080 mNm-1 to 50 mNm-1, but by changing the base-curing agent proportion of the elastomer from 10:1 to 30:1, the stiffness drops to 37 mNm-1. With these compliances, the proposed device will provide a new experimental tool for investigating force-dependent biological functions in sensory systems.
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Marsland R, England JL. Active regeneration unites high- and low-temperature features in cooperative self-assembly. Phys Rev E 2019; 98:022411. [PMID: 30253561 DOI: 10.1103/physreve.98.022411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Indexed: 12/29/2022]
Abstract
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) hydrolysis. The same is true for two-dimensional protein assemblies employed in the formation of vesicles from cellular membranes, which rely on ATP-hydrolyzing enzymes to rapidly disassemble upon completion of the process. Recent observations suggest that the nucleolus, p granules, and other three-dimensional membraneless organelles may also demand dissipation of chemical energy to maintain their fluidity. Cooperative binding plays a crucial role in the dynamics of these higher-dimensional structures, but is absent from classic models of one-dimensional cytoskeletal assembly. In this paper, we present a thermodynamically consistent model of active regeneration with cooperative assembly, and compute the maximum turnover rate and minimum disassembly time as a function of the chemical driving force and the binding energy. We find that these driven structures resemble different equilibrium states above and below the nucleation barrier. In particular, we show that the maximal acceleration under large binding energies unites infinite-temperature local fluctuations with low-temperature nucleation kinetics.
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Affiliation(s)
- Robert Marsland
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jeremy L England
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
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Nathwani B, Shih WM, Wong WP. Force Spectroscopy and Beyond: Innovations and Opportunities. Biophys J 2018; 115:2279-2285. [PMID: 30447991 PMCID: PMC6302248 DOI: 10.1016/j.bpj.2018.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 10/08/2018] [Accepted: 10/25/2018] [Indexed: 12/26/2022] Open
Abstract
Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream biology has been impeded by technical and conceptual barriers, including limitations in our ability to 1) easily measure and apply mechanical forces to biological systems, 2) scale these measurements from single-molecule characterization to more complex biomolecular systems, and 3) model and interpret biophysical data in a coherent way across length scales that span single molecules to cells to multicellular organisms. In this manuscript, through a look at historical and recent developments in force spectroscopy techniques and a discussion of a few exemplary open problems in cellular biomechanics, we aim to identify research opportunities that will help us reach our goal of a more complete and integrated understanding of the role of force and mechanics in biological systems.
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Affiliation(s)
- Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts
| | - Wesley P Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
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28
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Tridgett M, Lozano L, Passaretti P, Desai NR, Proctor TJ, Little HA, Logan RT, Arkill KP, Oppenheimer PG, Dafforn TR. Dye Aggregate-Mediated Self-Assembly of Bacteriophage Bioconjugates. Bioconjug Chem 2018; 29:3705-3714. [PMID: 30347978 DOI: 10.1021/acs.bioconjchem.8b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
One of the central themes of biomolecular engineering is the challenge of exploiting the properties of biological materials. Part of this challenge has been uncovering and harnessing properties of biological components that only emerge following their ordered self-assembly. One biomolecular building block that has received significant interest in the past decade is the M13 bacteriophage. There have been a number of recent attempts to trigger the ordered assembly of M13 bacteriophage into multivirion structures, relying on the innate tendency of M13 to form liquid crystals at high concentrations. These, in general, yield planar two-dimensional materials. Presented here is the production of multivirion assemblies of M13 bacteriophage via the chemical modification of its surface by the covalent attachment of the xanthene-based dye tetramethylrhodamine (TMR) isothiocyanate (TRITC). We show that TMR induces the formation of three-dimensional aster-like assemblies of M13 by providing "adhesive" action between bacteriophage particles through the formation of H-aggregates (face-to-face stacking of dye molecules). We also show that the H-aggregation of TMR is greatly enhanced by covalent attachment to M13 and is enhanced further still upon the ordered self-assembly of M13, leading to the suggestion that M13 could be used to promote the self-assembly of dyes that form J-aggregates, a desirable arrangement of fluorescent dye, which has interesting optical properties and potential applications in the fields of medicine and light harvesting technology.
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Affiliation(s)
| | | | | | | | - Toby J Proctor
- Research Department of Haematology , UCL Medical School, Royal Free Campus , Rowland Hill Street , London , NW3 2PF , United Kingdom
| | | | | | - Kenton P Arkill
- School of Medicine , University of Nottingham , Nottingham , NG7 2UH , United Kingdom
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29
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Molina A, Scheibel T, Humenik M. Nanoscale Patterning of Surfaces via DNA Directed Spider Silk Assembly. Biomacromolecules 2018; 20:347-352. [DOI: 10.1021/acs.biomac.8b01333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Elting MW, Suresh P, Dumont S. The Spindle: Integrating Architecture and Mechanics across Scales. Trends Cell Biol 2018; 28:896-910. [PMID: 30093097 PMCID: PMC6197898 DOI: 10.1016/j.tcb.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 01/28/2023]
Abstract
The spindle segregates chromosomes at cell division, and its task is a mechanical one. While we have a nearly complete list of spindle components, how their molecular-scale mechanics give rise to cellular-scale spindle architecture, mechanics, and function is not yet clear. Recent in vitro and in vivo measurements bring new levels of molecular and physical control and shed light on this question. Highlighting recent findings and open questions, we introduce the molecular force generators of the spindle, and discuss how they organize microtubules into diverse architectural modules and give rise to the emergent mechanics of the mammalian spindle. Throughout, we emphasize the breadth of space and time scales at play, and the feedback between spindle architecture, dynamics, and mechanics that drives robust function.
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Affiliation(s)
- Mary Williard Elting
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Physics, Riddick Hall 258A, Box 8202, North Carolina State University, Raleigh, NC 27695, USA; These authors contributed equally
| | - Pooja Suresh
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; These authors contributed equally
| | - Sophie Dumont
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Cellular & Molecular Pharmacology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA.
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31
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Tang VW. Cell-cell adhesion interface: orthogonal and parallel forces from contraction, protrusion, and retraction. F1000Res 2018; 7. [PMID: 30345009 PMCID: PMC6173117 DOI: 10.12688/f1000research.15860.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2018] [Indexed: 01/22/2023] Open
Abstract
The epithelial lateral membrane plays a central role in the integration of intercellular signals and, by doing so, is a principal determinant in the emerging properties of epithelial tissues. Mechanical force, when applied to the lateral cell-cell interface, can modulate the strength of adhesion and influence intercellular dynamics. Yet the relationship between mechanical force and epithelial cell behavior is complex and not completely understood. This commentary aims to provide an investigative look at the usage of cellular forces at the epithelial cell-cell adhesion interface.
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Affiliation(s)
- Vivian W Tang
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, 61801, USA
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32
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Ghanti D, Patra S, Chowdhury D. Molecular force spectroscopy of kinetochore-microtubule attachment in silico: Mechanical signatures of an unusual catch bond and collective effects. Phys Rev E 2018; 97:052414. [PMID: 29906871 DOI: 10.1103/physreve.97.052414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Indexed: 06/08/2023]
Abstract
Measurement of the lifetime of attachments formed by a single microtubule (MT) with a single kinetochore (kt) in vitro under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past, the physical origin of this apparently counterintuitive phenomenon was traced to the nature of the force dependence of the (de)polymerization kinetics of the MTs. Here, first the same model MT-kt attachment is subjected to external tension that increases linearly with time until rupture occurs. In our force-ramp experiments in silico, the model displays the well known "mechanical signatures" of a catch bond probed by molecular force spectroscopy. Exploiting this evidence, we have further strengthened the analogy between MT-kt attachments and common ligand-receptor bonds in spite of the crucial differences in their underlying physical mechanisms. We then extend the formalism to model the stochastic kinetics of an attachment formed by a bundle of multiple parallel microtubules with a single kt considering the effect of rebinding under force-clamp and force-ramp conditions. From numerical studies of the model we predict the trends of variation of the mean lifetime and mean rupture force with the increasing number of MTs in the bundle. Both the mean lifetime and the mean rupture force display nontrivial nonlinear dependence on the maximum number of MTs that can attach simultaneously to the same kt.
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Affiliation(s)
- Dipanwita Ghanti
- Department of Physics, Indian Institute of Technology Kanpur, 208016, India
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33
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Parreno J, Cheng C, Nowak RB, Fowler VM. The effects of mechanical strain on mouse eye lens capsule and cellular microstructure. Mol Biol Cell 2018; 29:1963-1974. [PMID: 30088796 PMCID: PMC6232967 DOI: 10.1091/mbc.e18-01-0035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mouse eye lens was used as a model for multiscale transfer of loads. In the lens, compressive strain is distributed across specific lens tissue microstructures, including the extracellular capsule, as well as the epithelial and fiber cells. The removal of high loads resulted in complete recovery of most, but not all, microstructures. The understanding of multiscale load transfer within complex soft tissues is incomplete. The eye lens is ideal for multiscale mechanical studies because its principal function is to fine-focus light at different distances onto the retina via shape changes. The biomechanical function, resiliency, and intricate microstructure of the lens makes it an excellent nonconnective soft tissue model. We hypothesized that strain applied onto whole-lens tissue leads to deformation of specific microstructures and that this deformation is reversible following load removal. For this examination, mouse lenses were compressed by sequential application of increasing load. Using confocal microscopy and quantitative image analysis, we determined that axial strain ≥10% reduces capsule thickness, expands epithelial cell area, and separates fiber cell tips at the anterior region. At the equatorial region, strain ≥6% increases fiber cell widths. The effects of strain on lens epithelial cell area, capsule thickness, and fiber cell widths are reversible following the release from strain. However, the separation of fiber cell tips is irreversible at high loads. This irreversible separation between fiber cell tips leads to incomplete whole-lens resiliency. The lens is an accessible biomechanical model system that provides new insights on multiscale transfer of loads in soft tissues.
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Affiliation(s)
- Justin Parreno
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037
| | - Catherine Cheng
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037
| | - Roberta B Nowak
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037
| | - Velia M Fowler
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037
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34
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Nanoscale mechanobiology of cell adhesions. Semin Cell Dev Biol 2017; 71:53-67. [PMID: 28754443 DOI: 10.1016/j.semcdb.2017.07.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 12/16/2022]
Abstract
Proper physiological functions of cells and tissues depend upon their abilities to sense, transduce, integrate, and generate mechanical and biochemical signals. Although such mechanobiological phenomena are widely observed, the molecular mechanisms driving these outcomes are still not fully understood. Cell adhesions formed by integrins and cadherins receptors are key structures that process diverse sources of signals to elicit complex mechanobiological responses. Since the nanoscale is the length scale at which molecules interact to relay force and information, the understanding of cell adhesions at the nanoscale level is important for grasping the inner logics of cellular decision making. Until recently, the study of the biological nanoscale has been restricted by available molecular and imaging tools. Fortunately, rapid technological advances have increasingly opened up the nanoscale realm to systematic investigations. In this review, we discuss current insights and key open questions regarding the nanoscale structure and function relationship of cell adhesions, focusing on recent progresses in characterizing their composition, spatial organization, and cytomechanical operation.
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35
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Li K, Zhang C, Qiu L, Gao L, Zhang X. Advances in Application of Mechanical Stimuli in Bioreactors for Cartilage Tissue Engineering. TISSUE ENGINEERING PART B-REVIEWS 2017; 23:399-411. [PMID: 28463576 DOI: 10.1089/ten.teb.2016.0427] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Articular cartilage (AC) is the weight-bearing tissue in diarthroses. It lacks the capacity for self-healing once there are injuries or diseases due to its avascularity. With the development of tissue engineering, repairing cartilage defects through transplantation of engineered cartilage that closely matches properties of native cartilage has become a new option for curing cartilage diseases. The main hurdle for clinical application of engineered cartilage is how to develop functional cartilage constructs for mass production in a credible way. Recently, impressive hyaline cartilage that may have the potential to provide capabilities for treating large cartilage lesions in the future has been produced in laboratories. The key to functional cartilage construction in vitro is to identify appropriate mechanical stimuli. First, they should ensure the function of metabolism because mechanical stimuli play the role of blood vessels in the metabolism of AC, for example, acquiring nutrition and removing wastes. Second, they should mimic the movement of synovial joints and produce phenotypically correct tissues to achieve the adaptive development between the micro- and macrostructure and function. In this article, we divide mechanical stimuli into three types according to forces transmitted by different media in bioreactors, namely forces transmitted through the liquid medium, solid medium, or other media, then we review and summarize the research status of bioreactors for cartilage tissue engineering (CTE), mainly focusing on the effects of diverse mechanical stimuli on engineered cartilage. Based on current researches, there are several motion patterns in knee joints; but compression, tension, shear, fluid shear, or hydrostatic pressure each only partially reflects the mechanical condition in vivo. In this study, we propose that rolling-sliding-compression load consists of various stimuli that will represent better mechanical environment in CTE. In addition, engineers often ignore the importance of biochemical factors to the growth and development of engineered cartilage. In our point of view, only by fully considering synergistic effects of mechanical and biochemical factors can we find appropriate culture conditions for functional cartilage constructs. Once again, rolling-sliding-compression load under appropriate biochemical conditions may be conductive to realize the adaptive development between the structure and function of engineered cartilage in vitro.
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Affiliation(s)
- Ke Li
- Tianjin Key Laboratory of Design and Intelligent Control of the Advanced Mechatronical System, School of Mechanical Engineering, Tianjin University of Technology , Tianjin, China
| | - Chunqiu Zhang
- Tianjin Key Laboratory of Design and Intelligent Control of the Advanced Mechatronical System, School of Mechanical Engineering, Tianjin University of Technology , Tianjin, China
| | - Lulu Qiu
- Tianjin Key Laboratory of Design and Intelligent Control of the Advanced Mechatronical System, School of Mechanical Engineering, Tianjin University of Technology , Tianjin, China
| | - Lilan Gao
- Tianjin Key Laboratory of Design and Intelligent Control of the Advanced Mechatronical System, School of Mechanical Engineering, Tianjin University of Technology , Tianjin, China
| | - Xizheng Zhang
- Tianjin Key Laboratory of Design and Intelligent Control of the Advanced Mechatronical System, School of Mechanical Engineering, Tianjin University of Technology , Tianjin, China
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36
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Emergence of Distinct Spatial Patterns in Cellular Automata with Inertia: A Phase Transition-Like Behavior. ENTROPY 2017. [DOI: 10.3390/e19030102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Lesoway MP. The future of Evo-Devo: the inaugural meeting of the Pan American Society for evolutionary developmental biology. Evol Dev 2016; 18:71-7. [PMID: 26773456 DOI: 10.1111/ede.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
What is the future of evolutionary developmental biology? This question and more were discussed at the inaugural meeting for the Pan American Society for Evolutionary Developmental Biology, held August 5-9, 2015, in Berkeley, California, USA. More than 300 participants attended the first meeting of the new society, representing the current diversity of Evo-Devo. Speakers came from throughout the Americas, presenting work using an impressive range of study systems, techniques, and approaches. Current research draws from themes including the role of gene regulatory networks, plasticity and the role of the environment, novelty, population genetics, and regeneration, using new and emerging techniques as well as traditional tools. Multiple workshops and a discussion session covered subjects both practical and theoretical, providing an opportunity for members to discuss the current challenges and future directions for Evo-Devo. The excitement and discussion generated over the course of the meeting demonstrates the current dynamism of the field, suggesting that the future of Evo-Devo is bright indeed.
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Affiliation(s)
- Maryna P Lesoway
- Department of Biology, McGill University, 1205 Avenue Dr Penfield, Montreal, QC, Canada, H3A-1B1.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancon, Republic of Panama
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